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Commit 049569a4 authored by Studer Gabriel's avatar Studer Gabriel
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Merge branch 'release-4.3.1'

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Changes in Release 4.3.1
--------------------------------------------------------------------------------
* Several minor bug fixes, improvements
Changes in Release 4.3.0
--------------------------------------------------------------------------------
......
......@@ -12,7 +12,7 @@ cmake_policy(SET CMP0060 NEW)
set (QMEAN_VERSION_MAJOR 4)
set (QMEAN_VERSION_MINOR 3)
set (QMEAN_VERSION_PATCH 0)
set (QMEAN_VERSION_PATCH 1)
set (QMEAN_VERSION_STRING ${QMEAN_VERSION_MAJOR}.${QMEAN_VERSION_MINOR}.${QMEAN_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
......@@ -74,7 +74,7 @@ set(PYTHON_MODULE_PATH "python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/si
setup_boost()
find_package(OPENSTRUCTURE 2.3.0 REQUIRED
find_package(OPENSTRUCTURE 2.4.0 REQUIRED
COMPONENTS mol seq seq_alg mol_alg conop db)
include_directories(${Boost_INCLUDE_DIRS}
......
......@@ -70,9 +70,9 @@ copyright = u'2016-2020, Gabriel Studer'
# built documents.
#
# The short X.Y version.
release = '4.3.0'
release = '4.3.1'
# The full version, including alpha/beta/rc tags.
release = '4.3.0'
release = '4.3.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......
......@@ -164,6 +164,7 @@ RUN set -eo pipefail; \
/usr/bin/sed -i 's/\/cluster\/toolkit\/production\/bioprogs\/psipred\/bin/\/usr\/local\/bin/g' scripts/HHPaths.pm; \
/usr/bin/sed -i 's/\/cluster\/toolkit\/production\/bioprogs\/psipred\/data/\/usr\/local\/data/g' scripts/HHPaths.pm; \
/usr/bin/sed -i 's/\/cluster\/toolkit\/production\/bioprogs\/blast\/bin/\/usr\/local\/bin/g' scripts/HHPaths.pm; \
/usr/bin/sed -i 's/\/cluster\/databases\/dssp\/bin\/dsspcmbi//g' scripts/HHPaths.pm; \
_hhblts_cmke=""; \
if test ${OPT_FOR_CPU} -eq 0; then \
_hhblts_cmke="-DHAVE_SSE2=1"; \
......@@ -223,7 +224,7 @@ RUN set -eo pipefail; \
# Install OpenStructure
#
# Version can be switched via --build-arg OST_VERSION="<TAG|BRANCH>"
ARG OST_VERSION="2.2.0"
ARG OST_VERSION="2.3.0"
ENV VERSION_OPENSTRUCTURE=$OST_VERSION
RUN set -eo pipefail; \
# \
......@@ -286,7 +287,7 @@ RUN set -eo pipefail; \
# Install QMEAN
#
# Version can be switched via --build-arg QMEAN_VERSION="<TAG|BRANCH>"
ARG QMEAN_VERSION="4.2.0"
ARG QMEAN_VERSION="4.3.0"
ENV VERSION_QMEAN=$QMEAN_VERSION
RUN set -eo pipefail; \
# \
......
......@@ -105,12 +105,12 @@ downloaded by either pulling it yourself or let Docker pull it first time you
run it. To actively pull, use the following command:
```terminal
$ docker pull registry.scicore.unibas.ch/schwede/qmean:4.2.0
4.2.0: Pulling from schwede/qmean
$ docker pull registry.scicore.unibas.ch/schwede/qmean:latest
latest: Pulling from schwede/qmean
...
Digest: sha256:db53a753d46b2525051478f9fa273df2b47a69100663eb70d538b461d52743d5
Status: Downloaded newer image for registry.scicore.unibas.ch/schwede/qmean:4.2.0
registry.scicore.unibas.ch/schwede/qmean:4.2.0
Status: Downloaded newer image for registry.scicore.unibas.ch/schwede/qmean:latest
registry.scicore.unibas.ch/schwede/qmean:latest
$
```
......@@ -189,7 +189,7 @@ Having everything setup, you can score `model.pdb` with SEQRES data stored in
`seqres.fasta` using QMEANDisCo:
```terminal
docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 -v <PATH_TO_LOCAL_QMTL>:/qmtl registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py model.pdb --seqres seqres.fasta
docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 -v <PATH_TO_LOCAL_QMTL>:/qmtl registry.scicore.unibas.ch/schwede/qmean:latest run_qmean.py model.pdb --seqres seqres.fasta
```
Additionally to the mounts specified above, the current working directory
......@@ -199,7 +199,7 @@ as workdir.
The following gives more details on additional command line arguments:
```terminal
docker run registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py --help
docker run registry.scicore.unibas.ch/schwede/qmean:latest run_qmean.py --help
```
<a name="singularity"></a>Singularity
......@@ -208,7 +208,7 @@ docker run registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py --help
A Singularity Image can directly be pulled & build from our registry:
```terminal
singularity build qmean_container.sif docker://registry.scicore.unibas.ch/schwede/qmean:4.2.0
singularity build qmean_container.sif docker://registry.scicore.unibas.ch/schwede/qmean:latest
```
Singularity allows to directly access the current working directory from within the container,
......
......@@ -185,14 +185,11 @@ def GenerateEnergyGapPlot(energy, path):
ax.spines['top'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.set_xticks(xtick_positions, xtick_labels)
ax.set_xticks(xtick_positions)
ax.set_xticklabels(xtick_labels)
fig.savefig(path)
LSCORES_TABLE_HEADER='''\
This file contains local scores calculated by the QMEAN scoring function.
......
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