When I run computeMatrix, I have on ly this in the log file : 192.168.000.000 - - [03/oct./2017:10:16:07 +0200] "POST /galaxy/api/tools/deeptools_compute_matrix/build HTTP/1.1" 200 - "http://192.168.100.000:8080/galaxy?job_id=7e6a9fe53e29fc38&__identifer=tmmenbexqep" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:37.0) Gecko/20100101 Firefox/37.0" On the job working directory I have this in tool_script.sh : #!/bin/bash # The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin' ; computeMatrix --version > /data/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_38413 2>&1; ln -f -s "/data/galaxy-dist/database/files/080/dataset_80817.dat" "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw" && ln -f -s "/data/galaxy-dist/database/files/080/dataset_80593.dat" "MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed" && computeMatrix scale-regions --regionsFileName 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bed' --scoreFileName 'MACS2narrow_SamToBam_Bowtie_mapped_readsTrim__0.bw' --outFileName '/data/galaxy-dist/database/files/080/dataset_80995.dat' --numberOfProcessors "${GALAXY_SLOTS:-4}" --regionBodyLength 500 It seems to export the good path for executable. So I don't understand. In the galaxy_38413.sh : #!/bin/bash # The following block can be used by the job system # to ensure this script is runnable before actually attempting # to run it. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi GALAXY_SLOTS="1"; export GALAXY_SLOTS; export GALAXY_SLOTS PRESERVE_GALAXY_ENVIRONMENT="True" GALAXY_LIB="/data/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi GALAXY_VIRTUAL_ENV="/data/galaxy-dist/.venv" if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" \ -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" -a "$PRESERVE_GALAXY_ENVIRONMENT" = "True" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate" fi echo "$GALAXY_SLOTS" > '/data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_galaxy_slots' date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_start cd /data/galaxy-dist/database/job_working_directory/038/38413 rm -rf working; mkdir -p working; cd working; /data/galaxy-dist/database/job_working_directory/038/38413/tool_script.sh; return_code=$?; cd '/data/galaxy-dist/database/job_working_directory/038/38413'; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate" fi GALAXY_PYTHON=`command -v python` export PATH=$PATH:'/data/galaxy-dist/tool_dependency/_conda/envs/__samtools@1.3.1/bin' ; python "/data/galaxy-dist/database/job_working_directory/038/38413/set_metadata_c9AkjG.py" "/data/galaxy-dist/database/job_working_directory/038/38413/registry.xml" "/data/galaxy-dist/database/job_working_directory/038/38413/working/galaxy.json" "/data/galaxy-dist/database/job_working_directory/038/38413/metadata_in_HistoryDatasetAssociation_72822_Eqsgna,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_kwds_HistoryDatasetAssociation_72822_3VQ3be,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_out_HistoryDatasetAssociation_72822_TQg8Pq,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_results_HistoryDatasetAssociation_72822_ctopJa,/data/galaxy-dist/database/files/080/dataset_80995.dat,/data/galaxy-dist/database/job_working_directory/038/38413/metadata_override_HistoryDatasetAssociation_72822_Izp4CZ" 5242880; sh -c "exit $return_code" echo $? > /data/galaxy-dist/database/job_working_directory/038/38413/galaxy_38413.ec date +"%s" > /data/galaxy-dist/database/job_working_directory/038/38413/__instrument_core_epoch_end May be my galaxy.ini in not well configured for conda. For the moment concerning conda in galaxy.ini, I have these lines uncommented : preserve_python_environment = legacy_and_local dependency_resolvers_config_file = config/dependency_resolvers_conf.xml 2017-10-03 9:53 GMT+02:00 Marius van den Beek <m.vandenbeek@gmail.com>:
Also upon re-reading I see that your dependency is being picked up from /usr/local/bin, which indicates that this isn't using conda at all. A small excerpt from the logs when you try to run the tool may be helpful to understand what is going on there.
Best, Marius
On 3 October 2017 at 09:29, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Julie,
any chance you are setting PYTHONPATH before starting galaxy's job handlers (a common place would the supervisor config, in case you're using that)? This will interfere with all python modules that are installed via conda.
Best, Marius
On 3 October 2017 at 09:13, julie dubois <dubjulie@gmail.com> wrote:
Dear Greg, I read your discussion with @bgruening and I think it's not exactly the same. Because in my case, The executable IS present in my galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin . The problem is far away in the execution when the tool (computeMatrix in my example) try to load the python module deeptools.computeMatrix. So is there a solution to discover where is the problem ?
Thanks
2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <ghv2@psu.edu>:
This looks like the issue I’ve recently seen as well - I just discussed this with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc. I’m using a work-around of creating the __deeptools conda env manually. In my case, I’m not installing the whole suite, just the bamCoverage tool from the TS -
https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599.... My work-around is to create the conda env manually:
$conda create -n __deeptools@2.5.1 deep tools=2.5.1
This env is created in the conda environment outside of Galaxy, so I just copy it to the conda environment I’ve configured for Galaxy. This works, but it seems there is some issue with the installation from the TS, so perhaps a more ling term fix is needed.
On Oct 2, 2017, at 8:59 AM, julie dubois <dubjulie@gmail.com> wrote:
Hi dev team,
I have a very big problem since I updated to galaxy 17.05 with deeptools from toolshed.
Due to a bug in galaxy 17.05 with toolshed installed tools (reported in this issue https://github.com/galaxyproject/galaxy/issues/4591), I re-installed deeptools to try to resolve it. Not resolved really but it's another problem. I temporarly bypassed it.
Here is my problem : I've installed deeptools from toolshed and when we try to use "compute matrix" for example, we have this error message :
Fatal error: Exit code 1 () Traceback (most recent call last): File "/usr/local/bin/computeMatrix", line 4, in <module> from deeptools.computeMatrix import main ImportError: No module named deeptools.computeMatrix
It seems that wrapper are installed but not the tool "deeptools".
For more information, here it's the way for the installation : search and install via toolshed Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a) Info in Manage tool dependencies : version=2.5.1, resolver=Conda, green check symbol in the line with a list of all deeptools.
Galaxy 17.05, commit cfabe37 (21 sept 2017)
I've tried to uninstall/reinstall dependencies with conda but without success.
Have you any idea to install the deeptools please ?
Thanks. Julie ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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