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Commit message:
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94 |
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added:
do-test.bash doit.bash fake macros.xml ncbi_fcs_adaptor.xml notes.txt planemo_job_conf.xml serve.log test-data/adaptor_report.tab test-data/clean_fasta.fa.gz test-data/fcsadaptor_prok_test.fa.gz test.log |
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| diff -r 000000000000 -r d55ad8533d58 do-test.bash --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/do-test.bash Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,15 @@ +#!/usr/bin/env bash + +export "PLANEMO_GLOBAL_CONFIG_PATH=/scratch/rico/.planemo" +export "PLANEMO_GLOBAL_WORKSPACE=/scratch/rico/.planemo" + +rm -rf /tmp/tmp* /scratch/rico/.planemo + +planemo \ + --verbose \ + test \ + --job_config_file=/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/planemo_job_conf.xml \ + --no_cleanup \ + --galaxy_root=/scratch/rico/galaxy 2>&1 \ + | tee test.log + |
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| diff -r 000000000000 -r d55ad8533d58 doit.bash --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/doit.bash Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,15 @@ +#!/usr/bin/env bash + +export "PLANEMO_GLOBAL_CONFIG_PATH=/scratch/rico/.planemo" +export "PLANEMO_GLOBAL_WORKSPACE=/scratch/rico/.planemo" + +rm -rf /tmp/tmp* /scratch/rico/.planemo + +planemo \ + --verbose \ + serve \ + --job_config_file=/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/planemo_job_conf.xml \ + --no_cleanup \ + --galaxy_root=/scratch/rico/galaxy 2>&1 \ + | tee serve.log + |
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| diff -r 000000000000 -r d55ad8533d58 fake --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fake Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,15 @@ +categories: +- Sequence Analysis +description: FCS-adaptor detects adaptor and vector contamination in genome sequences. +homepage_url: https://github.com/ncbi/fcs +long_description: | + FCS-adaptor detects adaptor and vector contamination in genome + sequences. FCS-adaptor is a high-throughput implementation of NCBI + VecScreen. The FCS-adaptor executable retrieves a Docker or Singularity + container and runs a pipeline to screen input sequences against a + non-redudant database of adaptors and vectors using stringent BLAST + searches and remove contaminants from your genome. +name: ncbi_fcs_adaptor +owner: richard-burhans +remote_repository_url: https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor +type: unrestricted |
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| diff -r 000000000000 -r d55ad8533d58 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,15 @@ +<macros> + <xml name="requirements"> + <requirements> + <container type="docker">ncbi/fcs-adaptor:@TOOL_VERSION@</container> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.5.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="edam_ontology"> + <edam_operations> + <edam_operation>operation_3187</edam_operation> + </edam_operations> + </xml> +</macros> |
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| diff -r 000000000000 -r d55ad8533d58 ncbi_fcs_adaptor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ncbi_fcs_adaptor.xml Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,68 @@ +<tool id="ncbi_fcs_adaptor" name="NCBI FCS Adaptor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>detects contamination from foreign organisms in genome sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + /app/fcs/bin/av_screen_x -o "\$(pwd)" '$tax' '$input' + ]]></command> + <inputs> + <param name="input" type="data" format="fasta" label="Input file (Fasta file)" help="To detect contamination from adaptors and vectors, a genome sequence in a fasta file."/> + <param name="tax" type="select" label="Choose the taxonomy"> + <option value="--euk" selected="true">Eukaryotes</option> + <option value="--prok">Prokaryotes</option> + </param> + <section name="advanced" title="Advanced options" expanded="false"> + <param name="optional_log" type="select" label="Choose additional logs" multiple="true" display="checkboxes"> + <option value="adaptor_log" selected="false">Adaptor log</option> + <option value="validate_fasta_log" selected="false">FASTA validation log</option> + </param> + </section> + </inputs> + <outputs> + <data name="adaptor_report" format="tabular" from_work_dir="fcs_adaptor_report.txt" label="${tool.name} on ${on_string}: Adaptor report"/> + <data name="clean_fasta" format="fasta" from_work_dir="cleaned_sequences/*.dat" label="${tool.name} on ${on_string}: Cleaned Fasta"/> + <data name="adaptor_log" format="txt" from_work_dir="fcs_adaptor.log" label="${tool.name} on ${on_string}: Adaptor log"> + <filter>advanced['optional_log'] is not None and 'adaptor_log' in advanced['optional_log'].split(',')</filter> + </data> + <data name="validate_fasta_log" format="txt" from_work_dir="validate_fasta.txt" label="${tool.name} on ${on_string}: FASTA validation log"> + <filter>advanced['optional_log'] is not None and 'validate_fasta_log' in advanced['optional_log'].split(',')</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="input" value="fcsadaptor_prok_test.fa.gz" ftype="fasta"/> + <param name="tax" value="--prok"/> + <output name="adaptor_report" file="adaptor_report.tab" ftype="tabular" /> + <output name="clean_fasta" decompress="true" file="clean_fasta.fa.gz" ftype="fasta" /> + </test> + <test expect_num_outputs="4"> + <param name="input" value="fcsadaptor_prok_test.fa.gz" ftype="fasta"/> + <param name="tax" value="--prok"/> + <param name="optional_log" value="adaptor_log,validate_fasta_log"/> + <output name="adaptor_report" file="adaptor_report.tab" ftype="tabular" /> + <output name="clean_fasta" decompress="true" file="clean_fasta.fa.gz" ftype="fasta" /> + <output name="adaptor_log"> + <assert_contents> + <has_text_matching expression="\bINFO \[workflow \] completed success\b" /> + </assert_contents> + </output> + <output name="validate_fasta_log"> + <assert_contents> + <has_size value="0" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + FCS-adaptor is a high-throughput implementation of NCBI VecScreen. FCS-adaptor runs a pipeline to screen input sequences against a non-redudant database of adaptors and vectors using stringent BLAST searches and remove contaminants from your genome. + + FCS-adaptor removes terminal and internal matches to foreign sequences. Sequences identified as mostly adaptor/vector are removed entirely. FCS-adaptor produces a tabular output with details on the contaminant sequences identified as well as a cleaned FASTA. + + Please see the wiki for more information. + + https://github.com/ncbi/fcs/wiki/FCS-adaptor + ]]></help> +</tool> |
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| diff -r 000000000000 -r d55ad8533d58 notes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/notes.txt Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,17 @@ +-rw-r--r-- 1 rico rico 0 Feb 22 20:46 fasta_validation_log.txt +-rw-r--r-- 1 rico rico 15015 Feb 22 20:46 adapter_log.txt +-rw-r--r-- 1 rico rico 1996423 Feb 22 20:46 cleaned.fa +-rw-r--r-- 1 rico rico 36 Feb 22 20:46 adapter_report.tabular + + +<!-- + $DOCKER run --init --name $CONTAINER --user "$(id -u):$(id -g)" -v $FASTA_DIRNAME:/sample-volume/ \ + -v $EXPANDED_OUTPUT:/output-volume/ $DOCKER_IMAGE \ + /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME + + singularity run $CONTAINER \ + --bind $FASTA_DIRNAME:/sample-volume/ \ + --bind $EXPANDED_OUTPUT:/output-volume/ \ + $SINGULARITY_IMAGE \ + /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME +--> |
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| diff -r 000000000000 -r d55ad8533d58 planemo_job_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_job_conf.xml Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<!-- A sample job config that explicitly configures job running the way it is + configured by default (if there is no explicit config). --> +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <destinations default="docker_local"> + <destination id="local" runner="local"/> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> + <param id="docker_sudo">false</param> + </destination> + </destinations> +</job_conf> |
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| diff -r 000000000000 -r d55ad8533d58 serve.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/serve.log Fri Mar 01 18:26:57 2024 +0000 |
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| b'@@ -0,0 +1,4332 @@\n+Created directory for Galaxy configuration [/tmp/tmpqrlh6ih1]\n+Writing dependency_resolvers_config_file to path /tmp/tmpqrlh6ih1/resolvers_conf.xml with contents [<dependency_resolvers>\n+ <tool_shed_packages />\n+ <conda auto_init="True" auto_install="True" ensure_channels="conda-forge,bioconda,defaults" prefix="/afs/bx.psu.edu/home/rico/miniconda3" condarc_override="/scratch/rico/.planemo/condarc" />\n+ <conda versionless="true" auto_init="True" auto_install="True" ensure_channels="conda-forge,bioconda,defaults" prefix="/afs/bx.psu.edu/home/rico/miniconda3" condarc_override="/scratch/rico/.planemo/condarc" />\n+</dependency_resolvers>\n+]\n+Writing tool_conf to path /tmp/tmpqrlh6ih1/tool_conf.xml with contents [<toolbox>\n+ <tool file="data_source/upload.xml" />\n+ <tool file="/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/ncbi_fcs_adaptor.xml" />\n+</toolbox>\n+]\n+Starting Galaxy with command [cd /scratch/rico/galaxy && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && echo "Set \\$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV" && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then echo "Virtual environment directory exists."; else echo "Virtual environment directory does not exist."; fi && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && echo "Set \\$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV" && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then echo "Virtual environment directory exists."; else echo "Virtual environment directory does not exist."; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && bash -c \'pwd\' && bash -c \'which python\' && bash -c \'which pip\' && bash -c \'echo $GALAXY_VIRTUAL_ENV\' && bash -c \'echo $VIRTUAL_ENV\' && bash -c \'ls -a\' && /scratch/rico/galaxy/run.sh $COMMON_STARTUP_ARGS --server-name main]\n+With environment variables:\n+============================\n+GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY="test_key"\n+GALAXY_CONFIG_OVERRIDE_ADMIN_USERS="planemo@galaxyproject.org,test@bx.psu.edu"\n+GALAXY_CONFIG_OVERRIDE_EXPOSE_DATASET_PATH="True"\n+GALAXY_CONFIG_OVERRIDE_COLLECT_OUTPUTS_FROM="job_working_directory"\n+GALAXY_CONFIG_OVERRIDE_ALLOW_PATH_PASTE="True"\n+GALAXY_CONFIG_OVERRIDE_CHECK_MIGRATE_TOOLS="False"\n+GALAXY_CONFIG_OVERRIDE_USE_CACHED_DEPENDENCY_MANAGER="True"\n+GALAXY_CONFIG_OVERRIDE_BRAND="Configured by Planemo"\n+GALAXY_CONFIG_OVERRIDE_STRICT_CWL_VALIDATION="True"\n+GALAXY_CONFIG_OVERRIDE_CLEANUP_JOB="never"\n+GALAXY_CONFIG_OVERRIDE_SINGLE_USER="planemo@galaxyproject.org"\n+GALAXY_CONFIG_OVERRIDE_SERVER_NAME="main"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_DIR_TEMPLATE="${ftp_upload_dir}"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_PURGE="False"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_DIR="/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/test-data"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_SITE="Test Data"\n+GALAXY_CONFIG_OVERRIDE_CHECK_UPLOAD_CONTENT="False"\n+GALAXY_CONFIG_OVERRIDE_TOOL_DEPENDENCY_DIR="/tmp/tmpqrlh6ih1/deps"\n+GALAXY_CONFIG_OVERRIDE_FILE_PATH="/tmp/tmpqrlh6ih1/files"\n+GALAXY_CONFIG_OVERRIDE_NEW_FILE_PATH="/tmp/tmpqrlh6ih1/tmp"\n+GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="/tmp/tmpqrlh6ih1/tool_conf.xml,/tmp/tmpqrlh6ih1/shed_tools_conf.xml"\n+GALAXY_CONFIG_OVERRIDE_TOOL_SHEDS_CONFIG_FILE="/tmp/tmpqrlh6ih1/tool_sheds_conf.xml"\n+GALAXY_CONFIG_OVERRIDE_MANAGE_DEPENDENCY_RELATIONSHIPS="False"\n+GALAXY_CONFIG_OVERRIDE_JOB_WORKING_DIRECTORY="/tmp/tmpqrlh6ih1/job_working_directory"\n+GALAXY_CONFIG_OVERRIDE_TEMPLATE_CACHE_PATH="/tmp/tmpqrlh6ih1/compiled_templates"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_TYPE="file"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_DATA_DIR="/tmp/tmpqrlh6ih1/citations/data"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_LOCK_DIR="/tmp/tmpqrlh6ih1/citations/lock"\n+GALAXY_CONFIG_OVERRIDE_DATABAS'..b"\n+==> /tmp/tmpqrlh6ih1/gravity/log/celery.log <==\n+[2024-02-23 15:01:35,002: INFO/main] Task galaxy.clean_object_store_caches[535f1714-1353-40ac-acee-799c6b05d637] received\n+[2024-02-23 15:01:35,002: DEBUG/main] TaskPool: Apply <function fast_trace_task at 0x7f9f1756ed90> (args:('galaxy.clean_object_store_caches', '535f1714-1353-40ac-acee-799c6b05d637', {'lang': 'py', 'task': 'galaxy.clean_object_store_caches', 'id': '535f1714-1353-40ac-acee-799c6b05d637', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '535f1714-1353-40ac-acee-799c6b05d637', 'parent_id': None, 'argsrepr': '()', 'kwargsrepr': '{}', 'origin': 'gen78504@laila', 'ignore_result': False, 'properties': {'correlation_id': '535f1714-1353-40ac-acee-799c6b05d637', 'reply_to': 'a834fe8d-fc9c-31a2-9791-be846a6fc4af', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '02332643-0c8b-4178-9919-02885eee82d3'}, 'reply_to': 'a834fe8d-fc9c-31a2-9791-be846a6fc4af', 'correlation_id': '535f1714-1353-40ac-acee-799c6b05d637', 'hostname': 'celery@laila', 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal', 'priority': 0, 'redelivered': None},... kwargs:{})\n+[2024-02-23 15:01:35,005: INFO/main] Successfully executed Celery task clean_object_store_caches to prune object store cache directories clean_object_store_caches to prune object store cache directories (0.552 ms)\n+[2024-02-23 15:01:35,040: INFO/main] Task galaxy.clean_object_store_caches[535f1714-1353-40ac-acee-799c6b05d637] succeeded in 0.03627739998046309s: None\n+\n+==> /tmp/tmpqrlh6ih1/gravity/log/celery-beat.log <==\n+[2024-02-23 15:06:34,480: DEBUG/MainProcess] beat: Synchronizing schedule...\n+[2024-02-23 15:06:34,482: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.\n+[2024-02-23 15:11:34,383: DEBUG/MainProcess] beat: Synchronizing schedule...\n+[2024-02-23 15:11:34,384: INFO/MainProcess] Scheduler: Sending due task clean-object-store-caches (galaxy.clean_object_store_caches)\n+[2024-02-23 15:11:34,400: DEBUG/MainProcess] galaxy.clean_object_store_caches sent. id->6eb22bfa-2bec-4d16-ba81-b677c429938a\n+[2024-02-23 15:11:34,400: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.\n+\n+==> /tmp/tmpqrlh6ih1/gravity/log/celery.log <==\n+[2024-02-23 15:11:35,103: INFO/main] Task galaxy.clean_object_store_caches[6eb22bfa-2bec-4d16-ba81-b677c429938a] received\n+[2024-02-23 15:11:35,104: DEBUG/main] TaskPool: Apply <function fast_trace_task at 0x7f9f1756ed90> (args:('galaxy.clean_object_store_caches', '6eb22bfa-2bec-4d16-ba81-b677c429938a', {'lang': 'py', 'task': 'galaxy.clean_object_store_caches', 'id': '6eb22bfa-2bec-4d16-ba81-b677c429938a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '6eb22bfa-2bec-4d16-ba81-b677c429938a', 'parent_id': None, 'argsrepr': '()', 'kwargsrepr': '{}', 'origin': 'gen78504@laila', 'ignore_result': False, 'properties': {'correlation_id': '6eb22bfa-2bec-4d16-ba81-b677c429938a', 'reply_to': 'a834fe8d-fc9c-31a2-9791-be846a6fc4af', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'f8974f4e-d12f-44c5-8432-dd8db2f74b43'}, 'reply_to': 'a834fe8d-fc9c-31a2-9791-be846a6fc4af', 'correlation_id': '6eb22bfa-2bec-4d16-ba81-b677c429938a', 'hostname': 'celery@laila', 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal', 'priority': 0, 'redelivered': None},... kwargs:{})\n+[2024-02-23 15:11:35,107: INFO/main] Successfully executed Celery task clean_object_store_caches to prune object store cache directories clean_object_store_caches to prune object store cache directories (0.548 ms)\n+[2024-02-23 15:11:35,107: INFO/main] Task galaxy.clean_object_store_caches[6eb22bfa-2bec-4d16-ba81-b677c429938a] succeeded in 0.0018642700742930174s: None\n" |
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| diff -r 000000000000 -r d55ad8533d58 test-data/adaptor_report.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adaptor_report.tab Fri Mar 01 18:26:57 2024 +0000 |
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| @@ -0,0 +1,5 @@ +#accession length action range name +KPN158_ctg010 251170 ACTION_TRIM 1..27 CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB01113.1:Illumina TruSeq UD/CD Adapter Trimming Read 1 +KPN158_ctg041 1411 ACTION_TRIM 81..150 CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB00753.1:Illumina TruSeq DNA HT and RNA HT i5 index D507 adapter (Oligonucleotide sequence copyright 2007-2012 Illumina, Inc. All rights reserved.) +KPN158_ctg047 1099 ACTION_TRIM 1047..1099 CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB01092.1:Rubicon Genomics ThruPLEX DNA-seq dual-index D504 +KPN158_ctg049 1061 ACTION_TRIM 1..67 CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB00753.1:Illumina TruSeq DNA HT and RNA HT i5 index D507 adapter (Oligonucleotide sequence copyright 2007-2012 Illumina, Inc. All rights reserved.) |
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| diff -r 000000000000 -r d55ad8533d58 test-data/clean_fasta.fa.gz |
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| Binary file test-data/clean_fasta.fa.gz has changed |
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| diff -r 000000000000 -r d55ad8533d58 test-data/fcsadaptor_prok_test.fa.gz |
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| Binary file test-data/fcsadaptor_prok_test.fa.gz has changed |
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| diff -r 000000000000 -r d55ad8533d58 test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.log Fri Mar 01 18:26:57 2024 +0000 |
| [ |
| b'@@ -0,0 +1,13578 @@\n+Created directory for Galaxy configuration [/tmp/tmpu7x63f_i]\n+Writing dependency_resolvers_config_file to path /tmp/tmpu7x63f_i/resolvers_conf.xml with contents [<dependency_resolvers>\n+ <tool_shed_packages />\n+ <conda auto_init="True" auto_install="True" ensure_channels="conda-forge,bioconda,defaults" prefix="/afs/bx.psu.edu/home/rico/miniconda3" condarc_override="/scratch/rico/.planemo/condarc" />\n+ <conda versionless="true" auto_init="True" auto_install="True" ensure_channels="conda-forge,bioconda,defaults" prefix="/afs/bx.psu.edu/home/rico/miniconda3" condarc_override="/scratch/rico/.planemo/condarc" />\n+</dependency_resolvers>\n+]\n+Writing tool_conf to path /tmp/tmpu7x63f_i/tool_conf.xml with contents [<toolbox>\n+ <tool file="data_source/upload.xml" />\n+ <tool file="/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/ncbi_fcs_adaptor.xml" />\n+</toolbox>\n+]\n+Starting Galaxy with command [cd /scratch/rico/galaxy && if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/scratch/rico/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && echo "Set \\$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV" && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then echo "Virtual environment directory exists."; else echo "Virtual environment directory does not exist."; fi && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /scratch/rico/.venv/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /scratch/rico/.venv/bin/python3; echo "Created virtualenv"; fi && echo "Set \\$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV" && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then echo "Virtual environment directory exists."; else echo "Virtual environment directory does not exist."; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && bash -c \'pwd\' && bash -c \'which python\' && bash -c \'which pip\' && bash -c \'echo $GALAXY_VIRTUAL_ENV\' && bash -c \'echo $VIRTUAL_ENV\' && bash -c \'ls -a\' && /scratch/rico/galaxy/run.sh $COMMON_STARTUP_ARGS --daemon]\n+With environment variables:\n+============================\n+GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY="test_key"\n+GALAXY_CONFIG_OVERRIDE_ADMIN_USERS="planemo@galaxyproject.org,test@bx.psu.edu"\n+GALAXY_CONFIG_OVERRIDE_EXPOSE_DATASET_PATH="True"\n+GALAXY_CONFIG_OVERRIDE_COLLECT_OUTPUTS_FROM="job_working_directory"\n+GALAXY_CONFIG_OVERRIDE_ALLOW_PATH_PASTE="True"\n+GALAXY_CONFIG_OVERRIDE_CHECK_MIGRATE_TOOLS="False"\n+GALAXY_CONFIG_OVERRIDE_USE_CACHED_DEPENDENCY_MANAGER="True"\n+GALAXY_CONFIG_OVERRIDE_BRAND="Configured by Planemo"\n+GALAXY_CONFIG_OVERRIDE_STRICT_CWL_VALIDATION="True"\n+GALAXY_CONFIG_OVERRIDE_CLEANUP_JOB="never"\n+GALAXY_CONFIG_OVERRIDE_SINGLE_USER="planemo@galaxyproject.org"\n+GALAXY_CONFIG_OVERRIDE_SERVER_NAME="main"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_DIR_TEMPLATE="${ftp_upload_dir}"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_PURGE="False"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_DIR="/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/test-data"\n+GALAXY_CONFIG_OVERRIDE_FTP_UPLOAD_SITE="Test Data"\n+GALAXY_CONFIG_OVERRIDE_CHECK_UPLOAD_CONTENT="False"\n+GALAXY_CONFIG_OVERRIDE_TOOL_DEPENDENCY_DIR="/tmp/tmpu7x63f_i/deps"\n+GALAXY_CONFIG_OVERRIDE_FILE_PATH="/tmp/tmpu7x63f_i/files"\n+GALAXY_CONFIG_OVERRIDE_NEW_FILE_PATH="/tmp/tmpu7x63f_i/tmp"\n+GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="/tmp/tmpu7x63f_i/tool_conf.xml,/tmp/tmpu7x63f_i/shed_tools_conf.xml"\n+GALAXY_CONFIG_OVERRIDE_TOOL_SHEDS_CONFIG_FILE="/tmp/tmpu7x63f_i/tool_sheds_conf.xml"\n+GALAXY_CONFIG_OVERRIDE_MANAGE_DEPENDENCY_RELATIONSHIPS="False"\n+GALAXY_CONFIG_OVERRIDE_JOB_WORKING_DIRECTORY="/tmp/tmpu7x63f_i/job_working_directory"\n+GALAXY_CONFIG_OVERRIDE_TEMPLATE_CACHE_PATH="/tmp/tmpu7x63f_i/compiled_templates"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_TYPE="file"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_DATA_DIR="/tmp/tmpu7x63f_i/citations/data"\n+GALAXY_CONFIG_OVERRIDE_CITATION_CACHE_LOCK_DIR="/tmp/tmpu7x63f_i/citations/lock"\n+GALAXY_CONFIG_OVERRIDE_DATABASE_AUTO_MI'..b'8 ? I 0:00 [kworker/66:1-events]\n+ 75874 ? I 0:00 [kworker/46:1-events]\n+ 75893 ? I 0:00 [kworker/47:1-events]\n+ 75894 pts/6 S+ 0:00 bash ./do-test.bash\n+ 75896 pts/6 S+ 0:11 /scratch/rico/.venv/bin/python3 /scratch/rico/.venv/bin/planemo --verbose test --job_config_file=/scratch/rico/galaxytools/tools/ncbi_fcs_adaptor/planemo_job_conf.xml --no_cleanup --galaxy_root=/scratch/rico/galaxy\n+ 75897 pts/6 S+ 0:00 tee test.log\n+ 76003 ? I 0:00 [kworker/60:0-events]\n+ 76006 ? I 0:00 [kworker/10:1-kdmflush]\n+ 76009 ? I 0:00 [kworker/2:1-events]\n+ 76104 ? Ss 0:00 /scratch/rico/.planemo/gx_venv_3/bin/python /scratch/rico/.planemo/gx_venv_3/bin/supervisord -c /tmp/tmpu7x63f_i/gravity/supervisor/supervisord.conf\n+ 76105 ? S 0:14 /scratch/rico/.planemo/gx_venv_3/bin/python /scratch/rico/.planemo/gx_venv_3/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external\n+ 76106 ? S 0:11 /scratch/rico/.planemo/gx_venv_3/bin/python /scratch/rico/.planemo/gx_venv_3/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /tmp/tmpu7x63f_i/gravity/celery-beat-schedule\n+ 76107 ? S 0:17 /scratch/rico/.planemo/gx_venv_3/bin/python /scratch/rico/.planemo/gx_venv_3/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b localhost:39427 --workers=1 --config python:galaxy.web_stack.gunicorn_config --preload\n+ 76309 ? S 0:00 /scratch/rico/.planemo/gx_venv_3/bin/python -c from multiprocessing.semaphore_tracker import main;main(7)\n+ 76310 ? Sl 0:26 /scratch/rico/.planemo/gx_venv_3/bin/python /scratch/rico/.planemo/gx_venv_3/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b localhost:39427 --workers=1 --config python:galaxy.web_stack.gunicorn_config --preload\n+ 76528 ? I 0:00 [kworker/106:1-events]\n+ 76594 ? I 0:00 [kworker/37:0-events]\n+ 76612 ? I 0:00 [kworker/84:2-cgroup_destroy]\n+ 76614 ? S 0:00 sleep 180\n+ 76631 ? I 0:00 [kworker/5:0-events]\n+ 76632 ? S 0:00 sleep 180\n+ 76703 ? I 0:00 [kworker/43:2-events]\n+ 76725 ? I 0:00 [kworker/35:0-events]\n+ 76744 ? I 0:00 [kworker/29:0]\n+ 76749 ? I 0:00 [kworker/31:1-rcu_gp]\n+ 76750 ? I 0:00 [kworker/32:0-events]\n+ 77043 ? I 0:00 [kworker/101:1]\n+ 77106 ? I 0:00 [kworker/u226:2-rpciod]\n+ 77127 ? I 0:00 [kworker/18:2-events]\n+ 77128 ? I< 0:00 [kworker/u229:1-xprtiod]\n+ 77195 ? I 0:00 [kworker/49:2-events]\n+ 77214 ? I 0:00 [kworker/28:2]\n+ 77215 ? I 0:00 [kworker/44:0-events]\n+ 77220 ? I 0:00 [kworker/33:2-events]\n+ 77234 ? I 0:00 [kworker/u224:2]\n+ 77317 ? I 0:00 [kworker/u225:0-events_unbound]\n+ 77318 pts/6 R+ 0:00 ps ax\n+104034 ? Sl 17:26 /data6/deepro/miniconda3/envs/dnanexus/bin/python -m ipykernel_launcher --f=/afs/bx.psu.edu/user/d/dzb5732/.local/share/jupyter/runtime/kernel-v2-97629et4BqJf1SGy3.json\n+Shut down\n+supervisord has terminated\n+engine.test returning [<planemo.test.results.StructuredData object at 0x7f4411ea56a0>]\n+No file specified for test_output_markdown, skipping test output.\n+No file specified for test_output_text, skipping test output.\n+No file specified for test_output_xunit, skipping test output.\n+No file specified for test_output_junit, skipping test output.\n+No file specified for test_output_allure, skipping test output.\n+Killing pid file [/scratch/rico/galaxy/main.pid]\n+pid_file exists? [False]\n+All 2 test(s) executed passed.\n+ncbi_fcs_adaptor (Test #1): passed\n+ncbi_fcs_adaptor (Test #2): passed\n+Exiting planemo with exit code [0]\n' |