diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
index 2defeaab3edf4195e3c17e6fd3fc76fb9c9a5536..d8d6f2916ca0c3747f240c99d386278cb4c3dda5
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
pangenome
assembly/container/assemblySC.sif
assembly/.snakemake
-assembly/rulegraph.pdf
\ No newline at end of file
+assembly/rulegraph.pdf
+facienda.md
\ No newline at end of file
diff --git a/README.md b/README.md
old mode 100644
new mode 100755
index a1293f5307867828143b7bc0108a3607fdbd6cb8..1efd40ab1e1511b030bbff1686be9ef149f8eaad
--- a/README.md
+++ b/README.md
@@ -6,15 +6,39 @@ This folder contains two Snakemake workflows:
This is ongoing work, some things will change.
+
## Requirements
-Running the workflows requires [Snakemake](https://snakemake.readthedocs.io) and [Singularity](https://docs.sylabs.io/guides/latest/user-guide/). Both are installed on sciCORE and can be loaded as modules:
+On the sciCORE cluster, the pipeline is installed in the GROUP folder (**/scicore/home/gagneux/GROUP/PacbioSnake**) and ready to run.
+
+In other contexts, four things need to be set up before the pipeline can be run:
+
+ 1. Install Snakemake and Singularity
+ 2. Build the singularity container for the assembly pipeline
+ 3. Download the bakta database for genome annotation
+ 4. Pull the singularity container for the variant calling pipeline
+
+These steps are detailed below.
+
+
+### 1. Install Snakemake and Singularity
+As described on the [Snakemake](https://snakemake.readthedocs.io) and the [Singularity](https://docs.sylabs.io/guides/latest/user-guide/) sites.
+
+### 2. Build the singularity container for the assembly pipeline
```
-ml snakemake/6.6.1-foss-2021a
-ml Singularity/2.6.1
+cd assembly/container
+sudo singularity build assemblySC.sif assemblySC.def
```
-<img src="fig.png" width="50%" height="50%">
+
+### 3. Download the bakta database for genome annotation
+Light-weight (1.3 Gb) and full (33.1 Gb) databases for the *bakta* annotation tool can be downloaded from https://zenodo.org/records/7669534.
+The extracted folder should be located at assembly/resources/bakta_db/. Otherwise the path to the database can be modified in the assembly config file.
+
+
+### 4. Pull the singularity container for the variant calling pipeline
+```
+singularity pull docker://ghcr.io/pangenome/pggb:latest
+```
-*Section of a genome graph constructed from diverse MTBC genomes. It shows a nested structural variant: an IS6110 insertion within the TBD1 region.*
diff --git a/assembly/README.md b/assembly/README.md
old mode 100644
new mode 100755
index e55f57e4b037b60edb304ca1232d63c51e74ce15..f3b9227a112a4dd84e6ada1cfc39d7b57e94ef67
--- a/assembly/README.md
+++ b/assembly/README.md
@@ -6,16 +6,6 @@ The user needs to modify two things to run the workflow on her samples:
- the file config/config.yaml, which contains global options for the analysis
-## container
-Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
-
-
-```
-sudo singularity build assemblySMK.sif assemblySMK.def
-```
-
-
-
## samples.tsv
This is a tab-separated table with a header and two colums (see example): the first containing the sample names, which will be used to name the assemblies; the second with the absolute paths to the fastq files.
@@ -57,20 +47,30 @@ Important: singularity containers most be given access to the file locations thr
It's convenient to run snakemake in a screen, so we can do other things on scicore while it's running and occasionally check the progress.
-Important snakemake arguments:
- --jobs:
- --cluster
```
+# Open screen
screen -r assembly
+# Load Snakemake module
+ml snakemake/6.6.1-foss-2021a
+
+# Dry run
+
+
+# Real run
snakemake \
+ --config samples=1.5 \
+ --config outdir=./results \
+
--jobs 4
- -k \
- --latency-wait 60 \
--use-singularity --singularity-args "--bind /scicore/home/gagneux/GROUP/tbresearch/genomes/IN_PROGRESS/PacBio_genomes/Gagneux --bind /scicore/home/gagneux/stritt0001/TB/projects/pacbio_microscale/ --bind /scratch" \
- --cluster "sbatch --job-name=hifi_simul --cpus-per-task=4 --mem-per-cpu=4G --time=06:00:00 --qos=6hours --output=hifi_simul.o%j --error=hifi_simul.e%j"
+ --cluster "sbatch --job-name=pbassembly --cpus-per-task=4 --mem-per-cpu=4G --time=06:00:00 --qos=6hours --output=pbassembly.o%j --error=pbassembly.e%j"
-```
-Leave the screen with CTRL+a+d.
\ No newline at end of file
+# Leave the screen: CTRL+a+d
+
+# Return to the screen
+screen -r assembly
+
+```
\ No newline at end of file
diff --git a/assembly/config/config.yaml b/assembly/config/config.yaml
old mode 100644
new mode 100755
index 6b82edb7a11e09446e7191e42a029efdabee70dc..e3405c4772dbb36610b12b025c7e79d4038a9d36
--- a/assembly/config/config.yaml
+++ b/assembly/config/config.yaml
@@ -2,16 +2,16 @@
#
##############################
-project_directory: ./results
-output_prefix: pb_bernese
samples: config/samples.tsv
+outdir: ./results
+output_prefix: pb_bernese
ref:
genome_size: 4.4m
gbf: resources/H37Rv.gbf
-threads: 4
+bakta_db: resources/bakta_db
-keep_intermediate: "Yes"
+threads_per_job: 4
-mapreads: "No"
+keep_intermediate: "Yes"
diff --git a/assembly/config/samples.tsv b/assembly/config/samples.tsv
old mode 100644
new mode 100755
diff --git a/assembly/container/README.md b/assembly/container/README.md
old mode 100644
new mode 100755
index 83dbaae8f9adf1e2ad0ae042dff50d18f6b29cc6..d275f243313d4d84846fe3652a2be8627237f9f2
--- a/assembly/container/README.md
+++ b/assembly/container/README.md
@@ -34,8 +34,4 @@ conda env update --file environment.yml --prune
conda-lock --mamba -f environment.yml -p linux-64
conda-lock render -p linux-64 # allows using mamba create --file conda-linux-64.lock
-Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
-
-```
-sudo singularity build assemblySC.sif assemblySC.def
-```
\ No newline at end of file
+# The conda-linux-64.lock file is then used in assemblySC.def to build the container
diff --git a/assembly/container/assemblySC.def b/assembly/container/assemblySC.def
old mode 100644
new mode 100755
diff --git a/assembly/container/conda-linux-64.lock b/assembly/container/conda-linux-64.lock
old mode 100644
new mode 100755
index 7a872e3ed42f97c65dec979c6a9f988eafc100f5..15afcb4370e46a956f2723d167578752030f9614
--- a/assembly/container/conda-linux-64.lock
+++ b/assembly/container/conda-linux-64.lock
@@ -1,14 +1,12 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: 926ab17aedcc8b15a4be8db176a2c48cafc2fcb2c9f778737a63eb301e4e346e
+# input_hash: 2e06febb1f32f5d3e52edc793538b8ec57542223dda338ed8fb24ab1ce919365
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://repo.anaconda.com/pkgs/main/noarch/_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10.tar.bz2#3d11810264df927797876ba64fd2a714
https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-openblas.conda#9ddfcaef10d79366c90128f5dc444be8
-https://conda.anaconda.org/bioconda/linux-64/blast-legacy-2.2.26-h9ee0642_3.tar.bz2#b7fe67ef984501e8089a142f1f58ab2f
https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.08.22-h06a4308_0.conda#243d5065a09a3e85ab888c05f5b6445a
https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda#68eedfd9c06f2b0e6888d8db345b7f5b
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
https://repo.anaconda.com/pkgs/main/linux-64/libgfortran5-11.2.0-h1234567_1.conda#36a01a8c30e0cadf0d3e842c50b73f3b
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
https://repo.anaconda.com/pkgs/main/noarch/tzdata-2023c-h04d1e81_0.conda#29db02adf8808f7c64642cead3e28acd
@@ -19,21 +17,18 @@ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#
https://repo.anaconda.com/pkgs/main/noarch/sysroot_linux-64-2.17-h57e8cba_10.tar.bz2#daa11b19c141284d62536ba03f4c73aa
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-h031d066_1.tar.bz2#d4ed7d256f07678d839cadedd1d49443
-https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-h14c3975_1001.tar.bz2#b9e0ac5d747ceab0c8b85a470358e1a6
https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h7b6447c_0.conda#9303f4af7c004e069bae22bde8d800ee
https://repo.anaconda.com/pkgs/main/linux-64/c-ares-1.19.1-h5eee18b_0.conda#6cfbce52273a1cb888821f18ceaa83c4
-https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h4ac6f70_9.tar.bz2#919194f6f7d733afff4d3c6f54e08d07
https://repo.anaconda.com/pkgs/main/linux-64/expat-2.5.0-h6a678d5_0.conda#9a21d99d49a0a556cf9590430dec8ec0
https://repo.anaconda.com/pkgs/main/linux-64/giflib-5.2.1-h5eee18b_3.conda#aa7d64adb3cd8a75d398167f8c29afc3
https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-hdbdd923_4.tar.bz2#805f24f8e8109e5d3d16cfad6799af46
https://repo.anaconda.com/pkgs/main/linux-64/icu-58.2-he6710b0_3.conda#48cc14d5ad1a9bcd8dac17211a8deb8b
+https://repo.anaconda.com/pkgs/main/linux-64/isa-l-2.30.0-h7f8727e_0.conda#3acfe83a308fabe6cc27201716f50071
https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda#ac373800fda872108412d1ccfe3fa572
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlicommon-1.0.9-h5eee18b_7.conda#73357cb8fde4b92707ec575c8d8a7ebc
-https://repo.anaconda.com/pkgs/main/linux-64/libdb-6.2.32-h6a678d5_1.conda#3f0e8b19439efa7dad29eb8f6586f09e
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
https://repo.anaconda.com/pkgs/main/linux-64/libev-4.33-h7f8727e_1.conda#5065620db4393fb549f30114a33897d1
https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.4.4-h6a678d5_0.conda#06e288f9250abef59b9a367d151fc339
-https://repo.anaconda.com/pkgs/main/linux-64/libidn11-1.33-h7b6447c_0.conda#75d5c232628eb6701d7a491716243a1f
https://repo.anaconda.com/pkgs/main/linux-64/libnsl-2.0.0-h5eee18b_0.conda#55e3f1b0c2a70454cdf1a5d64fb44752
https://repo.anaconda.com/pkgs/main/linux-64/libopenblas-0.3.21-h043d6bf_0.conda#7f7324dcc3c4761a14f3e4ac443235a7
https://repo.anaconda.com/pkgs/main/linux-64/libunistring-0.9.10-h27cfd23_0.conda#5b6ed6cd1b1ca3a383daef1d6464d02a
@@ -43,18 +38,14 @@ https://repo.anaconda.com/pkgs/main/linux-64/libxcb-1.15-h7f8727e_0.conda#ada518
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2#67590caab043d6d7ffc371f9cced7848
https://repo.anaconda.com/pkgs/main/linux-64/lz4-c-1.9.4-h6a678d5_0.conda#53915e9402180a7f22ea619c41089520
-https://conda.anaconda.org/bioconda/linux-64/mafft-7.520-h031d066_2.tar.bz2#5623284463f08717e04eb6cf22242301
-https://conda.anaconda.org/bioconda/linux-64/muscle-5.1-h4ac6f70_3.tar.bz2#aea487cbcbed07625e0963472c4ac568
https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.4-h6a678d5_0.conda#5558eec6e2191741a92f832ea826251c
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
https://conda.anaconda.org/conda-forge/linux-64/ossuuid-1.6.2-hf484d3e_1000.tar.bz2#0ca24876ead80a9290d3936aea5fefb1
-https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-h031d066_2.tar.bz2#2adac5d4627dacbf16552a5e677a2a0b
https://repo.anaconda.com/pkgs/main/linux-64/pcre-8.45-h295c915_0.conda#b32ccc24d1d9808618c1e898da60f68d
-https://conda.anaconda.org/bioconda/linux-64/poa-2.0-h031d066_5.tar.bz2#7f92f2dd187e08868ffc6a9e12525f75
+https://conda.anaconda.org/bioconda/linux-64/piler-cr-1.06-h4ac6f70_4.tar.bz2#7347a0cd1ec5952af9566107bd7521bc
https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_6.tar.bz2#05eb05a68e41b289530c1f434a63fc73
https://repo.anaconda.com/pkgs/main/linux-64/xz-5.4.2-h5eee18b_0.conda#bcd31de48a0dcb44bc5b99675800c5cc
-https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.0-hf5e1c6e_3.tar.bz2#12923179bf2aa30867534a335c8d1a46
-https://conda.anaconda.org/bioconda/linux-64/clustalo-1.2.4-hdbdd923_7.tar.bz2#24fd3aaebe5ab116cb8fbddd34d62e39
+https://repo.anaconda.com/pkgs/main/linux-64/yaml-0.2.5-h7b6447c_0.conda#39fdbf4db769e494ffb06d95680c83d8
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlidec-1.0.9-h5eee18b_7.conda#5c31f3bd570dc4d7d799117c98aad6e3
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlienc-1.0.9-h5eee18b_7.conda#289179174f1216582a949b528d8224af
https://repo.anaconda.com/pkgs/main/linux-64/libedit-3.1.20221030-h5eee18b_0.conda#7c724a17739aceaf9d1633ff06962137
@@ -62,10 +53,10 @@ https://repo.anaconda.com/pkgs/main/linux-64/libevent-2.1.12-hdbd6064_1.conda#99
https://repo.anaconda.com/pkgs/main/linux-64/libidn2-2.3.4-h5eee18b_0.conda#2bd46aa89ec576ad787afcdd93e5eafb
https://repo.anaconda.com/pkgs/main/linux-64/libssh2-1.10.0-hdbd6064_2.conda#8a427fcc8b7c76b3b31543ffa77eb3b7
https://conda.anaconda.org/conda-forge/linux-64/openmp-8.0.1-0.tar.bz2#b35241079152e5cc891c99368395b2c6
+https://conda.anaconda.org/conda-forge/linux-64/pbzip2-1.1.13-h1fcc475_2.conda#e1bf3c0868789f3ddf5d1aeb47bc60a6
https://repo.anaconda.com/pkgs/main/linux-64/perl-5.32.1-0_h5eee18b_perl5.conda#bcfda54960f1646e408a6a4764b6530a
https://repo.anaconda.com/pkgs/main/linux-64/readline-8.2-h5eee18b_0.conda#be42180685cce6e6b0329201d9f48efb
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/bioconda/noarch/barrnap-0.9-hdfd78af_4.tar.bz2#da96203ff6df1a221c22dfde37951bdf
https://repo.anaconda.com/pkgs/main/linux-64/brotli-bin-1.0.9-h5eee18b_7.conda#1cc9b5d3edf7bf3247941f4b5c083242
https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.17-he4a0461_11.tar.bz2#23832bbbdfb4a2c05e2df120068b1c78
https://repo.anaconda.com/pkgs/main/linux-64/glib-2.69.1-he621ea3_2.conda#51cf1899782b3f3744aedd143fbc07f3
@@ -74,60 +65,48 @@ https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a9
https://repo.anaconda.com/pkgs/main/linux-64/krb5-1.20.1-h143b758_1.conda#cf1accc86321fa25d6b978cc748039ae
https://repo.anaconda.com/pkgs/main/linux-64/libcups-2.4.2-h2d74bed_1.conda#3f265c2172a9e8c90a74037b6fa13685
https://repo.anaconda.com/pkgs/main/linux-64/libllvm14-14.0.6-hdb19cb5_3.conda#aefea2b45cf32f12b4f1ffaa70aa3201
-https://repo.anaconda.com/pkgs/main/linux-64/libnghttp2-1.52.0-h2d74bed_1.conda#44dde36df87a5173faa6c94e0c652306
+https://repo.anaconda.com/pkgs/main/linux-64/libnghttp2-1.57.0-h2d74bed_0.conda#674871621300f54e7ffcf93e6e341638
https://repo.anaconda.com/pkgs/main/linux-64/libpng-1.6.39-h5eee18b_0.conda#f6aee38184512eb05b06c2e94d39ab22
https://repo.anaconda.com/pkgs/main/linux-64/libxml2-2.9.14-h74e7548_0.conda#2eafeb1cb5f00b034d150f3d70436e52
https://conda.anaconda.org/bioconda/linux-64/mummer-3.23-pl5321hdbdd923_16.tar.bz2#f6a61224c4c60a9d207125d52d17aed9
-https://conda.anaconda.org/conda-forge/linux-64/parallel-20230922-ha770c72_0.conda#dddd6d76147c54b06b138146e03f2918
-https://conda.anaconda.org/conda-forge/noarch/perl-algorithm-diff-1.201-pl5321hd8ed1ab_0.tar.bz2#4ec6c1ea1d18947663b8cdc5f63cb2bf
-https://conda.anaconda.org/conda-forge/noarch/perl-base-2.23-pl5321hd8ed1ab_0.tar.bz2#d0ae29661c8985b4e4a512e6973f7a3f
+https://conda.anaconda.org/conda-forge/linux-64/perl-b-cow-0.007-pl5321h166bdaf_0.tar.bz2#714283443387f417b6e93a13c3d1b006
https://conda.anaconda.org/conda-forge/linux-64/perl-capture-tiny-0.48-pl5321ha770c72_1.tar.bz2#4859b3d284090166394875e68184dc9c
-https://conda.anaconda.org/conda-forge/linux-64/perl-class-data-inheritable-0.09-pl5321ha770c72_0.conda#7f35030f8bdce01431ffbdea84ac60d1
https://conda.anaconda.org/conda-forge/noarch/perl-common-sense-3.75-pl5321hd8ed1ab_0.tar.bz2#ef70dc77e8b10bbb62f5e843b401ef0e
https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-bzip2-2.201-pl5321h166bdaf_0.tar.bz2#105e211458bf45fe64b6de5ae8283ba4
https://conda.anaconda.org/conda-forge/linux-64/perl-compress-raw-zlib-2.202-pl5321h166bdaf_0.tar.bz2#66176366c49e2f70b3a764bc744b5010
https://conda.anaconda.org/conda-forge/noarch/perl-constant-1.33-pl5321hd8ed1ab_0.tar.bz2#7f9fc9cfa08a3fe36ffcff820c65c3ac
-https://conda.anaconda.org/conda-forge/linux-64/perl-data-dumper-2.183-pl5321h166bdaf_0.tar.bz2#bc64b4d3f071a6a9db2023e696a0a2cb
-https://conda.anaconda.org/conda-forge/linux-64/perl-db_file-1.858-pl5321h166bdaf_0.tar.bz2#73e039a6ab8fbaa8b574097b4fcdd599
-https://conda.anaconda.org/conda-forge/linux-64/perl-devel-stacktrace-2.04-pl5321ha770c72_0.conda#66856471d98bc726af849694a7f6ea0f
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https://conda.anaconda.org/conda-forge/noarch/perl-sub-info-0.002-pl5321hd8ed1ab_0.tar.bz2#5b48dcf7df9e4e01d45de2c1f494d830
https://conda.anaconda.org/bioconda/noarch/perl-term-table-0.016-pl5321hdfd78af_0.tar.bz2#91a4c19686c0e1c8b34325664bd3eee4
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https://repo.anaconda.com/pkgs/main/linux-64/ply-3.11-py310h06a4308_0.conda#ef39417278853a79e018bafdefc88eda
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https://repo.anaconda.com/pkgs/main/noarch/python-tzdata-2023.3-pyhd3eb1b0_0.conda#479c037de0186d114b9911158427624e
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-2_cp310.tar.bz2#9e7160cd0d865e98f6803f1fe15c8b61
https://repo.anaconda.com/pkgs/main/linux-64/pytz-2023.3.post1-py310h06a4308_0.conda#7dc2266262aaf4d3a249c13b08fc43d4
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https://repo.anaconda.com/pkgs/main/linux-64/setuptools-68.0.0-py310h06a4308_0.conda#0717b3a5ea831485cad4faf3069be8dc
https://repo.anaconda.com/pkgs/main/noarch/six-1.16.0-pyhd3eb1b0_1.conda#34586824d411d36af2fa40e799c172d0
https://conda.anaconda.org/bioconda/linux-64/spades-3.15.5-h95f258a_1.tar.bz2#62ab35497479905dce6860525262104f
https://repo.anaconda.com/pkgs/main/noarch/threadpoolctl-2.2.0-pyh0d69192_0.conda#bbfdbae4934150b902f97daaf287efe2
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https://conda.anaconda.org/conda-forge/linux-64/edlib-1.3.9-py310hbf28c38_2.tar.bz2#8b584d7c371e4b39d00c2bd84c370bc3
https://conda.anaconda.org/bioconda/linux-64/flye-2.9.2-py310h2b6aa90_2.tar.bz2#a90ef68d45b94121fb2cf4223f74e565
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-https://conda.anaconda.org/bioconda/noarch/minced-0.4.2-hdfd78af_1.tar.bz2#eee6ac504430c045623a6616e13ba833
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https://repo.anaconda.com/pkgs/main/linux-64/numpy-1.26.0-py310heeff2f4_0.conda#d9205da8d1d3179199f77b7eb3041d1b
https://repo.anaconda.com/pkgs/main/linux-64/openpyxl-3.0.10-py310h5eee18b_0.conda#2e570037bdef24d2efeeccb6ea7cb14a
https://conda.anaconda.org/bioconda/noarch/perl-archive-tar-2.40-pl5321hdfd78af_0.tar.bz2#ef5f007762b5ad9425694104d7db4463
-https://conda.anaconda.org/bioconda/noarch/perl-bioperl-run-1.007003-pl5321hdfd78af_0.tar.bz2#5b7b092efda407c9af1981426d83f3f5
https://conda.anaconda.org/conda-forge/noarch/perl-business-isbn-3.007-pl5321hd8ed1ab_0.tar.bz2#a7a3d7614e1a73b8d9c20030651d6006
+https://conda.anaconda.org/bioconda/noarch/perl-config-general-2.65-pl5321hdfd78af_0.tar.bz2#5db2b44f2e5ae5a525805860088f89d4
https://conda.anaconda.org/conda-forge/noarch/perl-file-chdir-0.1011-pl5321hd8ed1ab_0.tar.bz2#c057570093f9298e9c5e4391877f2301
-https://conda.anaconda.org/bioconda/noarch/perl-http-date-6.06-pl5321hdfd78af_0.tar.bz2#dbf1658443c214ea04fce36312d7efe3
https://conda.anaconda.org/bioconda/noarch/perl-json-4.10-pl5321hdfd78af_0.tar.bz2#05467eeb1e57206d8dddf31c3128cd00
-https://conda.anaconda.org/bioconda/noarch/perl-test-most-0.38-pl5321hdfd78af_0.tar.bz2#af484f1f44bf33bb0a6ab33e109ab8cb
+https://conda.anaconda.org/bioconda/linux-64/perl-params-validate-1.31-pl5321h031d066_2.tar.bz2#6083e6722b58a73ebdcc572450ac0669
+https://conda.anaconda.org/conda-forge/linux-64/perl-readonly-2.05-pl5321ha770c72_0.tar.bz2#4a5fedeb429a9cb12b528ac60a5b5009
+https://conda.anaconda.org/bioconda/noarch/perl-statistics-basic-1.6611-pl5321hdfd78af_3.tar.bz2#78d401cc1d995de60b2b220e3804c535
https://conda.anaconda.org/bioconda/noarch/perl-test2-suite-0.000145-pl5321hdfd78af_0.tar.bz2#c07db9debdb82d45be8a2115f5eb952d
https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-1.02-pl5321hd8ed1ab_0.tar.bz2#3e3fac6ffef3fcda271b5511aecacaa8
https://repo.anaconda.com/pkgs/main/linux-64/pillow-9.4.0-py310h6a678d5_0.conda#8b3af83284248cad7e4632d2d2e66ba7
+https://conda.anaconda.org/bioconda/linux-64/pyhmmer-0.10.2-py310h4b81fae_0.tar.bz2#eff7291e182ce0f912f52451692eca2a
https://conda.anaconda.org/bioconda/noarch/pymummer-0.11.0-pyhdfd78af_1.tar.bz2#6941d8dec72ed06363dc79005ffaab36
https://conda.anaconda.org/bioconda/linux-64/pysam-0.21.0-py310h41dec4a_1.tar.bz2#9af70a0f7f85e62d8262bcb3c439a7e8
https://repo.anaconda.com/pkgs/main/noarch/python-dateutil-2.8.2-pyhd3eb1b0_0.conda#211ee00320b08a1ac9fea6677649f6c9
https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.9-py310h0dbaff4_4.tar.bz2#6084757a32153104e5d0720633b641b0
https://repo.anaconda.com/pkgs/main/linux-64/qt-main-5.15.2-h7358343_9.conda#d3eac069d7e4e93b866a07c2274c9ee7
-https://conda.anaconda.org/bioconda/linux-64/samtools-1.17-hd87286a_2.tar.bz2#7023989c21e5be8f32b1e4d43136dc36
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.18-h50ea8bc_1.tar.bz2#7a53b527d66566e2bd8d436766e9c39e
https://repo.anaconda.com/pkgs/main/linux-64/sip-6.6.2-py310h6a678d5_0.conda#28f9d07c459f080064a83f9ff84274e3
-https://conda.anaconda.org/bioconda/linux-64/viennarna-2.6.4-py310pl5321h6cc9453_0.tar.bz2#1d8581821ec82e02c4c1bfe7419dd8df
https://conda.anaconda.org/bioconda/noarch/bio_assembly_refinement-0.5.1-py_2.tar.bz2#b7d00fded241f99f8c8be3e062c81fed
https://repo.anaconda.com/pkgs/main/linux-64/biopython-1.78-py310h7f8727e_0.conda#1ff7a99b3368b82138cfe4e5b774ab75
https://repo.anaconda.com/pkgs/main/linux-64/bottleneck-1.3.5-py310ha9d4c09_0.conda#d2eff72acd7c666bc90875d7eb44b924
+https://repo.anaconda.com/pkgs/main/linux-64/brotlipy-0.7.0-py310h7f8727e_1002.conda#a8dfa5aefcc49d5e78000b16d2b7714e
https://repo.anaconda.com/pkgs/main/linux-64/contourpy-1.0.5-py310hdb19cb5_0.conda#9b1e392241c60302f830fe4446f6c722
+https://repo.anaconda.com/pkgs/main/linux-64/cryptography-41.0.3-py310hdda0065_0.conda#131e70e5d2c2e70438f8a751c0bae3c4
https://repo.anaconda.com/pkgs/main/linux-64/h5py-3.9.0-py310he06866b_0.conda#c6e6cb698b250453d693bf8c38aa4b22
-https://repo.anaconda.com/pkgs/main/linux-64/numexpr-2.8.4-py310h757a811_1.conda#8ea1c8006e56ca735fb3785f3e4c2110
+https://repo.anaconda.com/pkgs/main/linux-64/numexpr-2.8.7-py310h286c3b5_0.conda#194aa6cc6d8f3b796ca1bdf94302d11f
https://conda.anaconda.org/bioconda/linux-64/perl-alien-build-2.48-pl5321hec16e2b_0.tar.bz2#8b1ea03a11ce6b27945962c47013f93e
-https://conda.anaconda.org/bioconda/noarch/perl-bio-asn1-entrezgene-1.73-pl5321hdfd78af_3.tar.bz2#1fa1e8f39aad93a6dc5a07b5bbb0d648
-https://conda.anaconda.org/bioconda/noarch/perl-bio-coordinate-1.007001-pl5321hdfd78af_3.tar.bz2#e85ab6482178c1510bcb6d4339ad98ac
-https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-phylo-paml-1.7.3-pl5321hdfd78af_3.tar.bz2#6d6d8eb0deb2e754811767358989c8df
-https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-clustalw-1.7.4-pl5321hdfd78af_3.tar.bz2#f248e955dd6d2cac60b844cb6df7d68f
-https://conda.anaconda.org/bioconda/noarch/perl-file-listing-6.16-pl5321hdfd78af_0.tar.bz2#aee1982ba098bb88b04a68f6e06dd825
+https://conda.anaconda.org/bioconda/linux-64/perl-gd-2.76-pl5321h5b5514e_1.tar.bz2#e7f25ce5adc500ce63dd0302aef8057a
https://conda.anaconda.org/conda-forge/linux-64/perl-uri-5.17-pl5321ha770c72_0.conda#847c007d5f4a59b356a9cd577010b89c
-https://conda.anaconda.org/conda-forge/noarch/perl-xml-sax-expat-0.51-pl5321hd8ed1ab_0.tar.bz2#34e0bfb1064f174a93db74d0f8060603
https://repo.anaconda.com/pkgs/main/linux-64/pyqt5-sip-12.11.0-py310h6a678d5_1.conda#b82aa11de791880fef887aba52fb1235
+https://conda.anaconda.org/bioconda/linux-64/pyrodigal-2.3.0-py310h4b81fae_1.tar.bz2#19a1e732253bca42c469310ecf2f7488
https://repo.anaconda.com/pkgs/main/linux-64/qt-webengine-5.15.9-hd2b0992_4.conda#ed674e212597b93fffa1afc90a3e100c
-https://repo.anaconda.com/pkgs/main/linux-64/scipy-1.11.1-py310heeff2f4_0.conda#7d9f847145da9b1aa4e13dd814c2b35e
+https://repo.anaconda.com/pkgs/main/linux-64/scipy-1.11.3-py310heeff2f4_0.conda#b1682989a8d79aeb36d2cd9d9cc36663
+https://repo.anaconda.com/pkgs/main/linux-64/zstandard-0.19.0-py310h5eee18b_0.conda#91ffd92050e57ada4c065435845010c2
https://conda.anaconda.org/bioconda/noarch/circlator-1.5.5-py_2.tar.bz2#93076e12d4889e077bb01271ddf3ecbf
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https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-base-3.7.2-py310h1128e8f_0.conda#8ec7618696a8c5b49c1a9ece8a2ce056
-https://repo.anaconda.com/pkgs/main/linux-64/pandas-2.0.3-py310h1128e8f_0.conda#5507f09aae226b2d92c465ea4f0bcfe8
+https://repo.anaconda.com/pkgs/main/linux-64/pandas-2.1.1-py310h1128e8f_0.conda#c4bd4c94c97ac74003acb2db7647b911
https://conda.anaconda.org/bioconda/linux-64/perl-alien-libxml2-0.17-pl5321hec16e2b_0.tar.bz2#4628ba7447031d6e4661732a2e7bdc64
-https://conda.anaconda.org/bioconda/noarch/perl-http-message-6.36-pl5321hdfd78af_0.tar.bz2#a213d1308ffa8e0789996ae6ecda98ae
-https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.22-pl5321hdfd78af_0.tar.bz2#f3b44f2b9932c3def346e6ad9aabe43d
-https://conda.anaconda.org/bioconda/noarch/perl-www-robotrules-6.02-pl5321hdfd78af_4.tar.bz2#8305f4ed6306b1125a8c8caf2f05aec8
-https://conda.anaconda.org/bioconda/noarch/perl-xml-simple-2.25-pl5321hdfd78af_2.tar.bz2#dbe93edacb87099430c76e809bffa375
+https://repo.anaconda.com/pkgs/main/linux-64/pyopenssl-23.2.0-py310h06a4308_0.conda#0635167b62d52a894b72635739e5c7bc
https://repo.anaconda.com/pkgs/main/linux-64/qtwebkit-5.212-h4eab89a_4.conda#7317bbf3f3e66a0a02b07b860783ecff
https://repo.anaconda.com/pkgs/main/linux-64/scikit-learn-1.3.0-py310h1128e8f_0.conda#f2576482b7dcb9aea24815376fa24114
-https://conda.anaconda.org/bioconda/linux-64/perl-html-parser-3.81-pl5321h4ac6f70_1.tar.bz2#6ef96e2df04cabd48c4c888c1ec57523
-https://conda.anaconda.org/bioconda/noarch/perl-http-cookies-6.10-pl5321hdfd78af_0.tar.bz2#e814a81fb8024d2be457805250df690c
-https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.16-pl5321hdfd78af_0.tar.bz2#55e2a97aa9794010e0f1cedc1abb3f19
-https://conda.anaconda.org/bioconda/noarch/perl-http-negotiate-6.01-pl5321hdfd78af_4.tar.bz2#8a56e406990d3b84b89a50caf5f2811d
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https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2#1ce8ba66c656dbe547110201b1456797
https://repo.anaconda.com/pkgs/main/linux-64/pyqt-5.15.7-py310h6a678d5_1.conda#2084350b18db696c9bfa61401c3c62a6
+https://repo.anaconda.com/pkgs/main/linux-64/urllib3-1.26.16-py310h06a4308_0.conda#697436a05c160cbc08a61e12bc4ef1ff
https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-3.7.2-py310h06a4308_0.conda#d82ab76c17c1328f1966a198e72ee5e7
https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.0.8-hdbdd923_0.tar.bz2#3b58cf2b702f96d812c67466456fe251
-https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.67-pl5321hdfd78af_0.tar.bz2#9493077e9e1dae0017f0d4cd9baf7de6
+https://repo.anaconda.com/pkgs/main/linux-64/requests-2.31.0-py310h06a4308_0.conda#81e8293939370975e4887b12336e1b89
https://conda.anaconda.org/bioconda/linux-64/blast-2.14.1-pl5321h6f7f691_0.tar.bz2#717b2ae9b971e769e00b984e37fe8947
-https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-1.46-pl5321hdfd78af_1.tar.bz2#45b7ce435727456727f45b3e2121b23b
-https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-xpath-0.14-pl5321hdfd78af_2.tar.bz2#b959a7e6e307abaec3f06b0bc007809a
-https://conda.anaconda.org/bioconda/linux-64/t-coffee-12.00.7fb08c2-h26a2512_0.tar.bz2#a0e9a4fa83c8c2cb485f248cf5ec0a34
-https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2#1b4b260b45e9cac33fcb45918cda428b
-https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5321hdfd78af_5.tar.bz2#932416c9ba6a9af43609e04ec5952574
-https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2#a693939710e572d0f85f6058b534e319
-https://conda.anaconda.org/bioconda/noarch/prokka-1.14.6-pl5321hdfd78af_5.tar.bz2#6aea788d2ca74ab50d6816e7e0a75da2
+https://conda.anaconda.org/bioconda/linux-64/diamond-2.1.8-h43eeafb_0.tar.bz2#86ccdf1d01687ea915c5a805ab6aefbc
+https://conda.anaconda.org/bioconda/linux-64/ncbi-amrfinderplus-3.11.26-h283d18e_0.tar.bz2#531aa783d5e124a7168a0107a8ba6bd9
+https://conda.anaconda.org/bioconda/noarch/bakta-1.8.2-pyhdfd78af_1.tar.bz2#fcb919368132b69a0bba9157d4fa16a0
diff --git a/assembly/container/conda-lock.yml b/assembly/container/conda-lock.yml
old mode 100644
new mode 100755
index e2ae3a4a09caf5d45788f6fd81d8c0840bd2b5c9..5024cafbba29043e03e755ae5767d3064500a8ee
--- a/assembly/container/conda-lock.yml
+++ b/assembly/container/conda-lock.yml
@@ -1,4 +1,4 @@
-# This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT!
+# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT!
#
# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
# e.g. `conda env create`, the resulting environment will not change as new package versions become
@@ -9,8 +9,11 @@
# To update a single package to the latest version compatible with the version constraints in the source:
# conda-lock lock --lockfile conda-lock.yml --update PACKAGE
# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
-# conda-lock -f /home/cristobal/TB/projects/pacbio_microscale/gitlab/PacbioSnake/assembly/container/environment.yml --lockfile conda-lock.yml
+# conda-lock -f /home/cristobal/TB/projects/pacbio_microscale/gitlab/PacbioSnake/assembly/container/environment.yml -f environment.yml --lockfile conda-lock.yml
+version: 1
metadata:
+ content_hash:
+ linux-64: 2e06febb1f32f5d3e52edc793538b8ec57542223dda338ed8fb24ab1ce919365
channels:
- url: defaults
used_env_vars: []
@@ -20,1778 +23,1513 @@ metadata:
used_env_vars: []
- url: r
used_env_vars: []
- content_hash:
- linux-64: 926ab17aedcc8b15a4be8db176a2c48cafc2fcb2c9f778737a63eb301e4e346e
platforms:
- linux-64
sources:
- /home/cristobal/TB/projects/pacbio_microscale/gitlab/PacbioSnake/assembly/container/environment.yml
+ - environment.yml
package:
-- category: main
+- name: _libgcc_mutex
+ version: '0.1'
+ manager: conda
+ platform: linux-64
dependencies: {}
+ url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
hash:
md5: d7c89558ba9fa0495403155b64376d81
sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
- manager: conda
- name: _libgcc_mutex
+ category: main
optional: false
+- name: _sysroot_linux-64_curr_repodata_hack
+ version: '3'
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
- version: '0.1'
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/noarch/_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10.tar.bz2
hash:
md5: 3d11810264df927797876ba64fd2a714
sha256: 4cddefa5f393ddcb8a28426df841573016d5c2211219441d5870482eb98202aa
- manager: conda
- name: _sysroot_linux-64_curr_repodata_hack
+ category: main
optional: false
+- name: blas
+ version: '1.0'
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/noarch/_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10.tar.bz2
- version: '3'
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-openblas.conda
hash:
md5: 9ddfcaef10d79366c90128f5dc444be8
sha256: c85b5d0a336b5be0f415c71fd7fe2eca59e09f42221bfa684aafef5510ba5487
- manager: conda
- name: blas
+ category: main
optional: false
- platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-openblas.conda
- version: '1.0'
-- category: main
- dependencies: {}
- hash:
- md5: b7fe67ef984501e8089a142f1f58ab2f
- sha256: 64c7302072994df20f1a78e00c4baa7ca7c141f2b4935b79fb6a77758bbaf5bc
+- name: ca-certificates
+ version: 2023.08.22
manager: conda
- name: blast-legacy
- optional: false
platform: linux-64
- url: https://conda.anaconda.org/bioconda/linux-64/blast-legacy-2.2.26-h9ee0642_3.tar.bz2
- version: 2.2.26
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.08.22-h06a4308_0.conda
hash:
md5: 243d5065a09a3e85ab888c05f5b6445a
sha256: 1d721d9183dc6e5e6fd639827f6755aa3250d9c65d66f2108c4bc9d08208382a
- manager: conda
- name: ca-certificates
+ category: main
optional: false
+- name: ld_impl_linux-64
+ version: '2.38'
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.08.22-h06a4308_0.conda
- version: 2023.08.22
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda
hash:
md5: 68eedfd9c06f2b0e6888d8db345b7f5b
sha256: 0c7a6f340f4a9e15cc99b3c7e11f07c7670a9b881161739edd77753e5530fe31
- manager: conda
- name: ld_impl_linux-64
+ category: main
optional: false
- platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda
- version: '2.38'
-- category: main
- dependencies: {}
- hash:
- md5: d7c7e92a8ccc518709474dd3eda896b9
- sha256: 9971bbc316b2d56be275ccd796aedabecc414260fa0f46ee9dd1f1e40531a837
+- name: libgfortran5
+ version: 11.2.0
manager: conda
- name: libgfortran
- optional: false
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2
- version: 3.0.0
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libgfortran5-11.2.0-h1234567_1.conda
hash:
md5: 36a01a8c30e0cadf0d3e842c50b73f3b
sha256: 83df17eb4be4232b6616f4a713624fab63cd8c41ea9957941b85e302b8954268
- manager: conda
- name: libgfortran5
+ category: main
optional: false
+- name: libstdcxx-ng
+ version: 13.2.0
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libgfortran5-11.2.0-h1234567_1.conda
- version: 11.2.0
-- category: main
dependencies: {}
+ url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda
hash:
md5: 9172c297304f2a20134fc56c97fbe229
sha256: ab22ecdc974cdbe148874ea876d9c564294d5eafa760f403ed4fd495307b4243
- manager: conda
- name: libstdcxx-ng
+ category: main
optional: false
+- name: tzdata
+ version: 2023c
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda
- version: 13.2.0
-- category: main
dependencies: {}
+ url: https://repo.anaconda.com/pkgs/main/noarch/tzdata-2023c-h04d1e81_0.conda
hash:
md5: 29db02adf8808f7c64642cead3e28acd
sha256: aa653896749686eb15c28c719a57df597bced46f983b1fdbcc9db3e2db9cc795
- manager: conda
- name: tzdata
+ category: main
optional: false
+- name: kernel-headers_linux-64
+ version: 3.10.0
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/noarch/tzdata-2023c-h04d1e81_0.conda
- version: 2023c
-- category: main
dependencies:
_sysroot_linux-64_curr_repodata_hack: 3.*
+ url: https://repo.anaconda.com/pkgs/main/noarch/kernel-headers_linux-64-3.10.0-h57e8cba_10.tar.bz2
hash:
md5: e3bd6db33d8c10ba1f0ec109df503827
sha256: d499f6ee2be1a50514a7e415d15ad6f4d83db34db7faa0dcbf9a5f35cef494c2
- manager: conda
- name: kernel-headers_linux-64
+ category: main
optional: false
+- name: libgfortran-ng
+ version: 11.2.0
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/noarch/kernel-headers_linux-64-3.10.0-h57e8cba_10.tar.bz2
- version: 3.10.0
-- category: main
dependencies:
- __glibc: '>=2.17'
libgfortran5: 11.2.0.*
+ __glibc: '>=2.17'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libgfortran-ng-11.2.0-h00389a5_1.conda
hash:
md5: 7429b67ab7b1d7cb99b9d1f3ddaec6e3
sha256: 228ecd4c12468e9f5e2e1806e02309f83b9fdbc5860efd3b34afc8be52b86511
- manager: conda
- name: libgfortran-ng
+ category: main
optional: false
+- name: libgomp
+ version: 13.2.0
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libgfortran-ng-11.2.0-h00389a5_1.conda
- version: 11.2.0
-- category: main
dependencies:
- _libgcc_mutex: 0.1 conda_forge
+ _libgcc_mutex: '0.1'
+ url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda
hash:
md5: e2042154faafe61969556f28bade94b9
sha256: e1e82348f8296abfe344162b3b5f0ddc2f504759ebeb8b337ba99beaae583b15
- manager: conda
- name: libgomp
+ category: main
optional: false
+- name: _openmp_mutex
+ version: '4.5'
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda
- version: 13.2.0
-- category: main
dependencies:
- _libgcc_mutex: 0.1 conda_forge
+ _libgcc_mutex: '0.1'
libgomp: '>=7.5.0'
+ url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
hash:
md5: 73aaf86a425cc6e73fcf236a5a46396d
sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22
- manager: conda
- name: _openmp_mutex
+ category: main
optional: false
+- name: sysroot_linux-64
+ version: '2.17'
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
- version: '4.5'
-- category: main
dependencies:
_sysroot_linux-64_curr_repodata_hack: 3.*
- kernel-headers_linux-64: 3.10.0 h57e8cba_10
+ kernel-headers_linux-64: 3.10.0
+ url: https://repo.anaconda.com/pkgs/main/noarch/sysroot_linux-64-2.17-h57e8cba_10.tar.bz2
hash:
md5: daa11b19c141284d62536ba03f4c73aa
sha256: 58be41f285f25ecc3cb6fd6d5cb7965162c562d5b6d76ffdd4a7a774efc1347b
- manager: conda
- name: sysroot_linux-64
+ category: main
optional: false
+- name: libgcc-ng
+ version: 13.2.0
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/noarch/sysroot_linux-64-2.17-h57e8cba_10.tar.bz2
- version: '2.17'
-- category: main
dependencies:
- _libgcc_mutex: 0.1 conda_forge
+ _libgcc_mutex: '0.1'
_openmp_mutex: '>=4.5'
+ url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda
hash:
md5: c28003b0be0494f9a7664389146716ff
sha256: d361d3c87c376642b99c1fc25cddec4b9905d3d9b9203c1c545b8c8c1b04539a
- manager: conda
- name: libgcc-ng
+ category: main
optional: false
+- name: aragorn
+ version: 1.2.41
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda
- version: 13.2.0
-- category: main
dependencies:
libgcc-ng: '>=12'
+ url: https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-h031d066_1.tar.bz2
hash:
md5: d4ed7d256f07678d839cadedd1d49443
sha256: 1422d20a747fed42b4eb25488b14781863b6d3bc08dcc084c396f43e8c241e66
- manager: conda
- name: aragorn
+ category: main
optional: false
- platform: linux-64
- url: https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-h031d066_1.tar.bz2
- version: 1.2.41
-- category: main
- dependencies:
- libgcc-ng: '>=7.3.0'
- hash:
- md5: b9e0ac5d747ceab0c8b85a470358e1a6
- sha256: 8547d5716db0ce35bf5bbd96fa29cbf19cfe06e3a7b80d9bb5a9259a2e3dfdf8
+- name: bzip2
+ version: 1.0.8
manager: conda
- name: argtable2
- optional: false
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-h14c3975_1001.tar.bz2
- version: '2.13'
-- category: main
dependencies:
libgcc-ng: '>=7.3.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h7b6447c_0.conda
hash:
md5: 9303f4af7c004e069bae22bde8d800ee
sha256: d3fa503351a53692866182a3819fb28d105e32c25d177bf6a9444c4153215e0d
- manager: conda
- name: bzip2
+ category: main
optional: false
+- name: c-ares
+ version: 1.19.1
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h7b6447c_0.conda
- version: 1.0.8
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/c-ares-1.19.1-h5eee18b_0.conda
hash:
md5: 6cfbce52273a1cb888821f18ceaa83c4
sha256: 4d1eab39e366dc7b3016664ab1f6f24a61731fa7d420fd28fa24bb9bbbae03ed
- manager: conda
- name: c-ares
+ category: main
optional: false
- platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/c-ares-1.19.1-h5eee18b_0.conda
- version: 1.19.1
-- category: main
- dependencies:
- libgcc-ng: '>=12'
- libstdcxx-ng: '>=12'
- hash:
- md5: 919194f6f7d733afff4d3c6f54e08d07
- sha256: 5c158e31e5ae6fd58440499b1219e30b7ca782222d44d3725d6e41b4c111e78d
+- name: expat
+ version: 2.5.0
manager: conda
- name: clustalw
- optional: false
platform: linux-64
- url: https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h4ac6f70_9.tar.bz2
- version: '2.1'
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
libstdcxx-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/expat-2.5.0-h6a678d5_0.conda
hash:
md5: 9a21d99d49a0a556cf9590430dec8ec0
sha256: 6f4e78cdb27e60a1c1a269379bf48833a6ef9c3052731b2b009e79076ab40552
- manager: conda
- name: expat
+ category: main
optional: false
+- name: giflib
+ version: 5.2.1
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/expat-2.5.0-h6a678d5_0.conda
- version: 2.5.0
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/giflib-5.2.1-h5eee18b_3.conda
hash:
md5: aa7d64adb3cd8a75d398167f8c29afc3
sha256: 733084f0c4c2c5ef1723fab13f38b389d279c197f408fd724d399ef9c4ecfcc9
- manager: conda
- name: giflib
+ category: main
optional: false
+- name: hmmer
+ version: 3.3.2
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/giflib-5.2.1-h5eee18b_3.conda
- version: 5.2.1
-- category: main
dependencies:
libgcc-ng: '>=12'
libstdcxx-ng: '>=12'
+ url: https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-hdbdd923_4.tar.bz2
hash:
md5: 805f24f8e8109e5d3d16cfad6799af46
sha256: e75930cbaeb0ec2d8535bd7699f2e7fb1f0bf3314ebbda4c0a87561eef8f8958
- manager: conda
- name: hmmer
+ category: main
optional: false
+- name: icu
+ version: '58.2'
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-hdbdd923_4.tar.bz2
- version: 3.3.2
-- category: main
dependencies:
libgcc-ng: '>=7.3.0'
libstdcxx-ng: '>=7.3.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/icu-58.2-he6710b0_3.conda
hash:
md5: 48cc14d5ad1a9bcd8dac17211a8deb8b
sha256: fdf7a480fcb598d164cbd28d3ce015d7de52db30f76faf7a15fbb8bbc7b8c5af
+ category: main
+ optional: false
+- name: isa-l
+ version: 2.30.0
manager: conda
- name: icu
+ platform: linux-64
+ dependencies:
+ libgcc-ng: '>=7.5.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/isa-l-2.30.0-h7f8727e_0.conda
+ hash:
+ md5: 3acfe83a308fabe6cc27201716f50071
+ sha256: bed4f78cdc6e1a0e9c949b8eb2f81237f8c5d56478ac4e17414e6f6ce9cf0600
+ category: main
optional: false
+- name: jpeg
+ version: 9e
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/icu-58.2-he6710b0_3.conda
- version: '58.2'
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda
hash:
md5: ac373800fda872108412d1ccfe3fa572
sha256: 93c52c384566cf975a928b79563ae6f6cfe369252c6cbeb933dc174429efaa69
- manager: conda
- name: jpeg
+ category: main
optional: false
+- name: libbrotlicommon
+ version: 1.0.9
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda
- version: 9e
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libbrotlicommon-1.0.9-h5eee18b_7.conda
hash:
md5: 73357cb8fde4b92707ec575c8d8a7ebc
sha256: 3c819c1c8125c03f36f22bb766c18fff319f9f8916f441102d53d0eb8cebb03a
- manager: conda
- name: libbrotlicommon
+ category: main
optional: false
- platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libbrotlicommon-1.0.9-h5eee18b_7.conda
- version: 1.0.9
-- category: main
- dependencies:
- libgcc-ng: '>=11.2.0'
- libstdcxx-ng: '>=11.2.0'
- hash:
- md5: 3f0e8b19439efa7dad29eb8f6586f09e
- sha256: 7f8681b95ddbdb78a6bef70cd7c2e03bd8e3a04fbaa2709d46b38a600c001110
+- name: libdeflate
+ version: '1.18'
manager: conda
- name: libdb
- optional: false
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libdb-6.2.32-h6a678d5_1.conda
- version: 6.2.32
-- category: main
dependencies:
libgcc-ng: '>=12'
+ url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
hash:
md5: 6aa9c9de5542ecb07fdda9ca626252d8
sha256: 949d84ceea543802c1e085b2aa58f1d6cb5dd8cec5a9abaaf4e8ac65d6094b3a
- manager: conda
- name: libdeflate
+ category: main
optional: false
+- name: libev
+ version: '4.33'
+ manager: conda
platform: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
- version: '1.18'
-- category: main
dependencies:
libgcc-ng: '>=7.5.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libev-4.33-h7f8727e_1.conda
hash:
md5: 5065620db4393fb549f30114a33897d1
sha256: 75f04cf201848d58df127caf9f316f71e1103b28e00b5add9b0c8025e52d7569
- manager: conda
- name: libev
+ category: main
optional: false
+- name: libffi
+ version: 3.4.4
+ manager: conda
platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libev-4.33-h7f8727e_1.conda
- version: '4.33'
-- category: main
dependencies:
libgcc-ng: '>=11.2.0'
libstdcxx-ng: '>=11.2.0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.4.4-h6a678d5_0.conda
hash:
md5: 06e288f9250abef59b9a367d151fc339
sha256: 2ac2a8507a48fdf8ba71ab38b0843ca373782a4a0c6367775498843c24bbc08c
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-- category: main
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libstdcxx-ng: '>=11.2.0'
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libgcc-ng: '>=11.2.0'
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libgcc-ng: '>=11.2.0'
openssl: '>=3.0.8,<4.0a0'
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@@ -1800,303 +1538,222 @@ package:
xz: '>=5.2.5,<6.0a0'
zlib: '>=1.2.12,<1.3.0a0'
zstd: '>=1.5.2,<1.6.0a0'
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dependencies:
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libxcb: '>=1.14,<2.0a0'
libxml2: '>=2.9.12,<2.10.0a0'
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libgcc-ng: '>=7.5.0'
libxml2: '>=2.9.14,<2.10.0a0'
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-- category: main
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-- category: main
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-- category: main
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-- category: main
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-- category: main
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-- category: main
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-- category: main
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-- category: main
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+ perl: '>=5.32.1,<5.33.0a0'
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-- category: main
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-- category: main
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+ perl: '>=5.32.1,<6.0a0'
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-- category: main
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+ perl: '>=5.32.1,<6.0a0'
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@@ -2111,65 +1768,115 @@ package:
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xz: '>=5.4.2,<6.0a0'
zlib: '>=1.2.13,<1.3.0a0'
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-- category: main
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-- category: main
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-- category: main
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freetype: '>=2.10.4,<3.0a0'
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libxml2: '>=2.9.14,<2.10.0a0'
zlib: '>=1.2.13,<1.3.0a0'
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sha256: 30902d9e2575e212b14c798465ba8eea5cbd4024bc88e933893c9e29a2bf616d
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-- category: main
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gstreamer: '>=1.14.1,<2.0a0'
@@ -2194,16 +1913,16 @@ package:
libstdcxx-ng: '>=11.2.0'
libxcb: '>=1.14,<2.0a0'
zlib: '>=1.2.11,<1.3.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/gst-plugins-base-1.14.1-h6a678d5_1.conda
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sha256: e81dae03d17db2d5dbf9eb822fb15efe8dc0c5d768b499668a499114073369d8
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libgcc-ng: '>=11.2.0'
@@ -2212,91 +1931,103 @@ package:
libstdcxx-ng: '>=11.2.0'
openssl: '>=3.0.8,<4.0a0'
zlib: '>=1.2.13,<1.3.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/hdf5-1.12.1-h2b7332f_3.conda
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sha256: 0d856e9cee278a372273dd025cf6672e6dc9f632d2a36cf9b667f1beaa3b95c0
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-- category: main
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libzlib: '>=1.2.13,<1.3.0a0'
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xz: '>=5.2.6,<6.0a0'
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-- category: main
dependencies:
python: '>=3.10,<3.11.0a0'
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-- category: main
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libstdcxx-ng: '>=11.2.0'
python: '>=3.10,<3.11.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/kiwisolver-1.4.4-py310h6a678d5_0.conda
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-- category: main
dependencies:
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libgcc-ng: '>=7.3.0'
libtiff: '>=4.1.0,<5.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/lcms2-2.12-h3be6417_0.conda
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- url: https://repo.anaconda.com/pkgs/main/linux-64/lcms2-2.12-h3be6417_0.conda
- version: '2.12'
-- category: main
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libllvm14: '>=14.0.6,<14.1.0a0'
libstdcxx-ng: '>=11.2.0'
zlib: '>=1.2.13,<1.3.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libclang-14.0.6-default_hc6dbbc7_1.conda
hash:
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sha256: b0c313c723da06f405e7d053c7064f9403614a7fed6987b25ceeef976166dc03
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@@ -2304,407 +2035,412 @@ package:
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libtiff: '>=4.1.0,<5.0a0'
libwebp-base: 1.2.4.*
+ url: https://repo.anaconda.com/pkgs/main/linux-64/libwebp-1.2.4-h11a3e52_1.conda
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sha256: e3329353356fbee47b5947773bd555526459f51ea31982667f3c9a9e9d365535
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- name: libwebp
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platform: linux-64
- url: https://repo.anaconda.com/pkgs/main/linux-64/libwebp-1.2.4-h11a3e52_1.conda
- version: 1.2.4
-- category: main
dependencies:
libgcc-ng: '>=7.5.0'
python: '>=3.10,<3.11.0a0'
+ url: https://repo.anaconda.com/pkgs/main/linux-64/markupsafe-2.1.1-py310h7f8727e_0.conda
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-- category: main
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sha256: f3f473a60a6766a7f64447c0c7e49d0640db7f995255951e3477b5d21d144dc7
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libgcc-ng: '>=11.2.0'
libstdcxx-ng: '>=11.2.0'
openssl: '>=3.0.9,<4.0a0'
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sha256: c1aaab03aca20d50adf310a25f52623cf9cda0d59adaa73e0878225365cb6f54
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libopenblas: '>=0.3.21,<1.0a0'
libstdcxx-ng: '>=11.2.0'
python: '>=3.10,<3.11.0a0'
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- url: https://repo.anaconda.com/pkgs/main/linux-64/numpy-base-1.26.0-py310h8a23956_0.conda
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-- category: main
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python: '>=3.10,<3.11.0a0'
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-- category: main
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+ perl: '>=5.32.1,<6.0a0'
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- url: https://conda.anaconda.org/bioconda/noarch/perl-encode-locale-1.05-pl5321hdfd78af_7.tar.bz2
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-- category: main
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perl-constant: ''
perl-exporter: ''
perl-file-path: ''
perl-parent: ''
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-- category: main
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perl-compress-raw-zlib: '>=2.103'
perl-encode: ''
perl-scalar-list-utils: ''
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-- category: main
dependencies:
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libstdcxx-ng: '>=12'
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perl-types-serialiser: ''
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-- category: main
dependencies:
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tk: '>=8.6.12,<8.7.0a0'
zlib: '>=1.2.13,<1.3.0a0'
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pyfastaq: '>=3.10.0'
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-- category: main
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six: '>=1.5'
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zlib: '>=1.2.13,<1.3.0a0'
zstd: '>=1.5.2,<1.6.0a0'
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libzlib: '>=1.2.13,<1.3.0a0'
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sip: ''
toml: ''
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libxml2: '>=2.9.14,<2.10.0a0'
qt-main: '>=5.15.2,<5.16.0a0'
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python: '>=3.10,<3.11.0a0'
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bio_assembly_refinement: '>=0.4.0'
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@@ -3457,16 +3229,45 @@ package:
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samtools: ''
spades: ''
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python-dateutil: '>=2.7'
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sqlite: '>=3.38.5,<4.0a0'
zlib: '>=1.2.12,<1.3.0a0'
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@@ -3630,133 +3374,107 @@ package:
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scipy: '>=1.5.0'
threadpoolctl: '>=2.0.0'
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perl-alien-libxml2: 0.17.*
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pyqt: '>=5'
python: '>=3.10,<3.11.0a0'
tornado: '>=5'
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ca-certificates: ''
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@@ -3766,45 +3484,32 @@ package:
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perl-uri: ''
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perl-list-moreutils: ''
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- perl-xml-simple: ''
- prodigal: '>=2.6'
- tbl2asn-forever: '>=25.7'
- hash:
- md5: 6aea788d2ca74ab50d6816e7e0a75da2
- sha256: 654e7ab399907d0153052dc2f729d4b8db5de6c819686d2dbb8a4890782595c4
- manager: conda
- name: prokka
- optional: false
- platform: linux-64
- url: https://conda.anaconda.org/bioconda/noarch/prokka-1.14.6-pl5321hdfd78af_5.tar.bz2
- version: 1.14.6
-version: 1
diff --git a/assembly/container/environment.yml b/assembly/container/environment.yml
old mode 100644
new mode 100755
index cbebc99fe5b6188e4ad1fa532b91819b10d15387..adfc0d230e3be14cdf5a5a7ce5606bff32e6805f
--- a/assembly/container/environment.yml
+++ b/assembly/container/environment.yml
@@ -9,7 +9,7 @@ dependencies:
- samtools
- minimap2
- circlator
- - prokka
+ - bakta
- numpy
- scipy
- matplotlib
diff --git a/assembly/resources/H37Rv.gbf b/assembly/resources/H37Rv.gbf
old mode 100644
new mode 100755
diff --git a/assembly/workflow/Snakefile b/assembly/workflow/Snakefile
index b18e49cc3f391a9689a6e9ac30640ca861709c92..aa6153d077ed89bd3db43f6c1613b52272aa1fbc 100755
--- a/assembly/workflow/Snakefile
+++ b/assembly/workflow/Snakefile
@@ -13,22 +13,11 @@ include: "rules/annotate.smk"
include: "rules/summarize.smk"
-if config["mapreads"] == "yes":
-
- include: "rules/mapreads.smk"
-
- rule all:
- input:
- "results/read_summaries.tsv",
- "results/assembly_summaries.tsv",
- expand("results/{sample}/prokka/{sample}.gff", sample = samples.keys()),
- expand("results/{sample}/remapping/shortreads.bam", sample = samples.keys()),
- expand("results/{sample}/remapping/longreads.bam", sample = samples.keys())
-
-else:
- rule all:
- input:
- "results/read_summaries.tsv",
- "results/assembly_summaries.tsv",
- expand("results/{sample}/prokka/{sample}.gff", sample = samples.keys())
-
+include: "rules/mapreads.smk"
+
+rule all:
+ input:
+ config["outdir"] + "/read_summaries.tsv",
+ config["outdir"] + "/assembly_summaries.tsv",
+ expand(config["outdir"] + "/{sample}/{sample}.gff", sample = samples.keys()),
+ expand(config["outdir"] + "/{sample}/remapping/longreads.bam", sample = samples.keys())
diff --git a/assembly/workflow/rules/annotate.smk b/assembly/workflow/rules/annotate.smk
old mode 100644
new mode 100755
index 6a54e45b510503a3fc15fe2b431f00e3f11c1b6a..b8a55bf4fca81a628427bb6343c9ab6802833173
--- a/assembly/workflow/rules/annotate.smk
+++ b/assembly/workflow/rules/annotate.smk
@@ -1,27 +1,26 @@
-rule prokka:
- input: "results/{sample}/assembly.circularized.renamed.fasta"
- output: "results/{sample}/prokka/{sample}.gff"
- params:
- refgbf = config["ref"]["gbf"],
- asm = "{sample}",
- outdir = "results/{sample}/prokka"
- threads: config["threads"]
- envmodules: "prokka/1.14.5-gompi-2021a"
- shell:
- """
- prokka {input} \
- --force \
- --kingdom Bacteria \
- --genus Mycobacterium \
- --species tuberculosis \
- --strain {params.asm} \
- --addgenes \
- --proteins {params.refgbf} \
- --prefix {params.asm} \
- --locustag {params.asm} \
- --cpus {threads} \
- --outdir {params.outdir}
+rule bakta:
+ input: config["outdir"] + "/{sample}/assembly.circularized.renamed.fasta"
+ output: config["outdir"] + "/{sample}/{sample}.gff"
+ params:
+ bakta_db = config["bakta_db"],
+ refgbf = config["ref"]["gbf"],
+ asm = "{sample}",
+ outdir = config["outdir"] + "/{sample}/",
+ threads = config["threads_per_job"]
- """
+ shell:
+ """
+ bakta {input} \
+ --db {params.bakta_db} \
+ --prefix {params.asm} \
+ --genus Mycobacterium \
+ --species tuberculosis \
+ --strain {params.sample} \
+ --locus-tag {params.sample} \
+ --complete --compatible \
+ --proteins {params.refgbf} \
+ --keep-contig-headers \
+ --threads {params.threads}
+ """
diff --git a/assembly/workflow/rules/assemble.smk b/assembly/workflow/rules/assemble.smk
old mode 100644
new mode 100755
index cec994bf898b998688a0cfffcca43df045a1bfca..90d09fffe560fddd717c65c2a13874bebe025423
--- a/assembly/workflow/rules/assemble.smk
+++ b/assembly/workflow/rules/assemble.smk
@@ -1,11 +1,13 @@
rule flye:
input: lambda wildcards: samples[wildcards.sample].longread_fastq
- output: "results/{sample}/assembly.fasta", "results/{sample}/assembly_info.txt"
- threads: config["threads"]
+ output:
+ config["outdir"] + "/{sample}/flye/assembly.fasta",
+ config["outdir"] + "/{sample}/flye/assembly_info.txt"
+ threads: config["threads_per_job"]
params:
genome_size = config["ref"]["genome_size"],
- outdir = "results/{sample}"
+ outdir = config["outdir"] + "/{sample}/flye"
shell:
"""
@@ -15,4 +17,3 @@ rule flye:
--threads {threads} \
--out-dir {params.outdir}
"""
-
diff --git a/assembly/workflow/rules/circularize.smk b/assembly/workflow/rules/circularize.smk
old mode 100644
new mode 100755
index cce5cb3c333e117c913a5b61431727c5f7f1cea7..befa76253cbe02261ff3dd43b3addbd7845f5d9a
--- a/assembly/workflow/rules/circularize.smk
+++ b/assembly/workflow/rules/circularize.smk
@@ -1,11 +1,11 @@
rule circlator_mapreads:
input:
- assembly = 'results/{sample}/assembly.fasta',
+ assembly = config["outdir"] + "/{sample}/assembly.fasta",
reads = lambda wildcards: expand(samples[wildcards.sample].longread_fastq)
- output: "results/{sample}/circlator/01.mapreads.bam"
+ output: config["outdir"] + "/{sample}/circlator/01.mapreads.bam"
params:
- threads = config["threads"]
+ threads = config["threads_per_job"]
shell:
"""
@@ -14,10 +14,10 @@ rule circlator_mapreads:
"""
rule circlator_bam2reads:
- input: "results/{sample}/circlator/01.mapreads.bam"
- output: "results/{sample}/circlator/02.bam2reads.fasta"
+ input: config["outdir"] + "/{sample}/circlator/01.mapreads.bam"
+ output: config["outdir"] +"/{sample}/circlator/02.bam2reads.fasta"
params:
- output_pref = "results/{sample}/circlator/02.bam2reads"
+ output_pref = config["outdir"]+ "/{sample}/circlator/02.bam2reads"
shell:
"""
circlator bam2reads {input} {params.output_pref} --discard_unmapped
@@ -25,10 +25,10 @@ rule circlator_bam2reads:
"""
rule circlator_localassembly:
- input: "results/{sample}/circlator/02.bam2reads.fasta"
- output: "results/{sample}/circlator/03.assemble/assembly.fasta"
+ input: config["outdir"] + "/{sample}/circlator/02.bam2reads.fasta"
+ output: config["outdir"] + "/{sample}/circlator/03.assemble/assembly.fasta"
params:
- outdir = "results/{sample}/circlator/03.assemble",
+ outdir = config["outdir"] + "/{sample}/circlator/03.assemble",
threads = config["threads"]
shell:
"""
@@ -38,12 +38,12 @@ rule circlator_localassembly:
rule circlator_merge:
input:
- assembly = 'results/{sample}/assembly.fasta',
- localassembly = "results/{sample}/circlator/03.assemble/assembly.fasta"
- output: "results/{sample}/circlator/04.merge.fasta"
+ assembly = config["outdir"] + "/{sample}/assembly.fasta",
+ localassembly = config["outdir"] + "/{sample}/circlator/03.assemble/assembly.fasta"
+ output: config["outdir"] + "/{sample}/circlator/04.merge.fasta"
params:
- threads = config["threads"],
- output_pref = "results/{sample}/circlator/04.merge"
+ threads = config["threads_per_job"],
+ output_pref = config["outdir"] + "/{sample}/circlator/04.merge"
shell:
"""
circlator merge {input.assembly} {input.localassembly} {params.output_pref} --threads {params.threads}
@@ -51,10 +51,10 @@ rule circlator_merge:
"""
rule circlator_clean:
- input: "results/{sample}/circlator/04.merge.fasta"
- output: "results/{sample}/circlator/05.clean.fasta"
+ input: config["outdir"] + "/{sample}/circlator/04.merge.fasta"
+ output: config["outdir"] + "/{sample}/circlator/05.clean.fasta"
params:
- output_pref = "results/{sample}/circlator/05.clean"
+ output_pref = config["outdir"] + "/{sample}/circlator/05.clean"
shell:
"""
circlator clean {input} {params.output_pref}
@@ -62,10 +62,10 @@ rule circlator_clean:
"""
rule circlator_fixstart:
- input: "results/{sample}/circlator/05.clean.fasta"
- output: "results/{sample}/circlator/06.fixstart.fasta"
+ input: config["outdir"] + "/{sample}/circlator/05.clean.fasta"
+ output: config["outdir"] + "/{sample}/circlator/06.fixstart.fasta"
params:
- output_pref = "results/{sample}/circlator/06.fixstart"
+ output_pref = config["outdir"] + "/{sample}/circlator/06.fixstart"
shell:
"""
circlator fixstart {input} {params.output_pref}
@@ -74,12 +74,12 @@ rule circlator_fixstart:
rule rename:
input:
- assembly = "results/{sample}/circlator/06.fixstart.fasta"
+ assembly = config["outdir"] + "/{sample}/circlator/06.fixstart.fasta"
params:
prefix = "{sample}",
keep_intermediate = config["keep_intermediate"]
- output: "results/{sample}/assembly.circularized.renamed.fasta"
+ output: config["outdir"] + "/{sample}/assembly.circularized.renamed.fasta"
run:
diff --git a/assembly/workflow/rules/cleanup.smk b/assembly/workflow/rules/cleanup.smk
deleted file mode 100644
index d0d3b2a1a9ed1bea851396ecc8dac0eb73db5952..0000000000000000000000000000000000000000
--- a/assembly/workflow/rules/cleanup.smk
+++ /dev/null
@@ -1,7 +0,0 @@
- # Remove circlator and pilon intermediate results, which take up a lot of space
- if [ {params.keep_intermediate} == "No" ]; then
-
- rm results/{params.prefix}/noduplicates.fastq.gz
- rm -r results/{params.prefix}/pilon
- rm -r results/{params.prefix}/circlator
- fi
\ No newline at end of file
diff --git a/assembly/workflow/rules/common.smk b/assembly/workflow/rules/common.smk
old mode 100644
new mode 100755
diff --git a/assembly/workflow/rules/mapreads.smk b/assembly/workflow/rules/mapreads.smk
old mode 100644
new mode 100755
diff --git a/assembly/workflow/rules/readQC.smk b/assembly/workflow/rules/readQC.smk
old mode 100644
new mode 100755
index 2c5b50bdee08fe39c6cd707effbaf9ac56942486..da08f9a54eb68d76e472dd338e4d04b732dbf285
--- a/assembly/workflow/rules/readQC.smk
+++ b/assembly/workflow/rules/readQC.smk
@@ -1,9 +1,9 @@
rule longQC:
input: lambda wildcards: samples[wildcards.sample].longread_fastq
- output: "results/{sample}/longqc/QC_vals_longQC_sampleqc.json"
+ output: config["outdir"] + "/{sample}/longqc/QC_vals_longQC_sampleqc.json"
params:
- threads = config["threads"],
- outfolder = "results/{sample}/longqc/"
+ threads = config["threads_per_job"],
+ outfolder = config["outdir"] + "/{sample}/longqc/"
shell:
"""
diff --git a/assembly/workflow/rules/summarize.smk b/assembly/workflow/rules/summarize.smk
old mode 100644
new mode 100755
index 5a3cb7df60c1ae80111643990bf57268c152529c..c64e64a93fc6b81c80e7f3bf65b844de9e3be41f
--- a/assembly/workflow/rules/summarize.smk
+++ b/assembly/workflow/rules/summarize.smk
@@ -1,6 +1,7 @@
+
rule read_summary:
- input: expand("results/{sample}/longqc/QC_vals_longQC_sampleqc.json", sample = samples.keys())
- output: "results/read_summaries.tsv"
+ input: expand("{outdir}/{sample}/longqc/QC_vals_longQC_sampleqc.json", outdir = config["outdir"], sample = samples.keys())
+ output: config["outdir"] + "/read_summaries.tsv"
run:
import json
@@ -51,14 +52,16 @@ rule read_summary:
rule assembly_summaries:
- input: expand("results/{sample}/assembly_info.txt", sample = samples.keys())
- output: "results/assembly_summaries.tsv"
+ input: expand("{outdir}/{sample}/assembly_info.txt", outdir = config["outdir"], sample = samples.keys())
+ output:
+ summaries = config["outdir"] + "/assembly_summaries.tsv",
+ single_contig_assemblies = config["outdir"] + "/single_contig_samples.txt"
run:
header = ""
- outfile = open(output[0], "w")
+ outfile = open(output.summaries, "w")
- outfile_single_contigs = open("results/single_contig_samples.txt", "w")
+ outfile_single_contigs = open(output.single_contig_assemblies, "w")
for FILE in input:
diff --git a/fig.png b/fig.png
deleted file mode 100644
index 33c1362892d1b04809d97521f36318a7b06aa0d6..0000000000000000000000000000000000000000
Binary files a/fig.png and /dev/null differ
diff --git a/variantcalling/README.md b/variantcalling/README.md
old mode 100644
new mode 100755
index ce3013ac0eb8affd8714990f28e98e3a9a2f3344..5d5c07062c9a0280ca3fd240d834f4153a34f915
--- a/variantcalling/README.md
+++ b/variantcalling/README.md
@@ -1,5 +1,13 @@
# Variant calling workflow
+
+
+
+## container
+```
+singularity pull docker://ghcr.io/pangenome/pggb:latest
+```
+
## assemblies.txt
diff --git a/variantcalling/config/biopython.yaml b/variantcalling/config/biopython.yaml
old mode 100644
new mode 100755
diff --git a/variantcalling/config/config.yaml b/variantcalling/config/config.yaml
old mode 100644
new mode 100755
diff --git a/variantcalling/config/samples.txt b/variantcalling/config/samples.txt
old mode 100644
new mode 100755
diff --git a/variantcalling/workflow/Snakefile b/variantcalling/workflow/Snakefile
old mode 100644
new mode 100755
diff --git a/variantcalling/workflow/scripts/combine_assemblies.py b/variantcalling/workflow/scripts/combine_assemblies.py
old mode 100644
new mode 100755