From 54ad5b1baadb973fed48b7da5b4a9ddec9134ded Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 7 May 2021 15:00:51 +0200
Subject: [PATCH] workdir must be passed as absolute path
This is an inconvience in the ost hhblits binding which I plan to fix asap.
To avoid waiting for a new ost release, we just provide a documentation
solution here.
---
docker/qmean_qmeandisco_example/README.md | 7 ++++---
docker/qmeanbrane_example/README.md | 7 ++++---
docker/run_qmean.py | 2 +-
3 files changed, 9 insertions(+), 7 deletions(-)
diff --git a/docker/qmean_qmeandisco_example/README.md b/docker/qmean_qmeandisco_example/README.md
index e7fc2f2..c819202 100644
--- a/docker/qmean_qmeandisco_example/README.md
+++ b/docker/qmean_qmeandisco_example/README.md
@@ -22,11 +22,12 @@ sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/u
Normally, the container creates a temporary directory to store intermediate
results. If you want to investigate them, or access the sequence profiles,
-you can provide a working dir as argument. A directory gets created in the
-working dir for each unique SEQRES named after the md5 hash of the SEQRES:
+you can provide a working dir as argument (must be absolute path).
+A directory gets created in the working dir for each unique SEQRES named after
+the md5 hash of the SEQRES:
```terminal
-sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py model.pdb --method QMEAN --seqres targets.fasta --profiles query_hhblits_one.a3m query_hhblits_two.a3m --workdir my_workdir
+sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py model.pdb --method QMEAN --seqres targets.fasta --profiles query_hhblits_one.a3m query_hhblits_two.a3m --workdir $(pwd)/my_workdir
```
So far we only computed the QMEAN scoring function. QMEANDisCo includes
diff --git a/docker/qmeanbrane_example/README.md b/docker/qmeanbrane_example/README.md
index 7b263df..520b7cf 100644
--- a/docker/qmeanbrane_example/README.md
+++ b/docker/qmeanbrane_example/README.md
@@ -26,10 +26,11 @@ sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/u
Normally, the container creates a temporary directory to store intermediate
results. If you want to investigate them, or access the sequence profiles,
-you can provide a working dir as argument. A directory gets created in the
-working dir for each unique SEQRES named after the md5 hash of the SEQRES:
+you can provide a working dir as argument (must be absolute path).
+A directory gets created in the working dir for each unique SEQRES named
+after the md5 hash of the SEQRES:
```terminal
-sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py original_hhblits_alignment.pdb shift_in_front_helix_four.pdb shift_into_middle.pdb shift_towards_cter.pdb --method QMEANBrane --seqres targets.fasta --profiles query_hhblits.a3m --workdir my_workdir
+sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py original_hhblits_alignment.pdb shift_in_front_helix_four.pdb shift_into_middle.pdb shift_towards_cter.pdb --method QMEANBrane --seqres targets.fasta --profiles query_hhblits.a3m --workdir $(pwd)/my_workdir
```
diff --git a/docker/run_qmean.py b/docker/run_qmean.py
index a54c6b0..b2bdaf4 100755
--- a/docker/run_qmean.py
+++ b/docker/run_qmean.py
@@ -875,7 +875,7 @@ def _parse_args():
dest="workdir",
default=None,
help="Location for intermediate output, normally temporary. If given, "
- + "output remains for debug purposes",
+ + "output remains for debug purposes. Path must be absolute.",
)
parser.add_argument(
"--datefilter", dest="datefilter", default=None, help="Debug purposes"
--
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