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

@@ -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 

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
 ```
 

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"