diff --git a/Covid-19-Galaxy-container/All_Covid_tools.yaml b/Covid-19-Galaxy-container/All_Covid_tools.yaml deleted file mode 100644 index a93a8d1..0000000 --- a/Covid-19-Galaxy-container/All_Covid_tools.yaml +++ /dev/null @@ -1,478 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: true -tools: -- name: enumerate_charges - owner: bgruening - revisions: - - 2a868592ebcb - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: split_file_to_collection - owner: bgruening - revisions: - - e77b954f0da5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: openbabel_compound_convert - owner: bgruening - revisions: - - e6011617c748 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: openbabel_compound_convert - owner: bgruening - revisions: - - e6011617c748 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: rdock_rbcavity - owner: bgruening - revisions: - - 5f73eb32ddbf - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: openbabel_compound_convert - owner: bgruening - revisions: - - e6011617c748 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: text_processing - owner: bgruening - revisions: - - fb4ff3c42cd3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: split_file_to_collection - owner: bgruening - revisions: - - e77b954f0da5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: rdock_rbdock - owner: bgruening - revisions: - - 5f291eef9ef3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 830961c48e42 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: rdock_sort_filter - owner: bgruening - revisions: - - 784a9f7f079e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: split_file_to_collection - owner: bgruening - revisions: - - e77b954f0da5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: sucos_max_score - owner: bgruening - revisions: - - 2f110aef9b53 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 830961c48e42 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: split_file_to_collection - owner: bgruening - revisions: - - e77b954f0da5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: xchem_transfs_scoring - owner: bgruening - revisions: - - de29b4f35536 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: text_processing - owner: bgruening - revisions: - - fb4ff3c42cd3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: openbabel_filter - owner: bgruening - revisions: - - da0059ee548a - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: openbabel_change_title - owner: bgruening - revisions: - - 49d21d05f77c - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: jq - owner: iuc - revisions: - - 5ff75eb1a893 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 830961c48e42 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: sdf_to_tab - owner: bgruening - revisions: - - 40ff81f67f5e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: datamash_ops - owner: iuc - revisions: - - 562f3c677828 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastp - owner: iuc - revisions: - - a935cbdf1c0e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: nanoplot - owner: iuc - revisions: - - edbb6c5028f5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastqc - owner: devteam - revisions: - - 3e1cdf5406db - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: minimap2 - owner: iuc - revisions: - - 17e61517c166 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: multiqc - owner: iuc - revisions: - - b2f1f75d49c4 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: bwa - owner: devteam - revisions: - - 01ac0a5fedc3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtool_filter2 - owner: devteam - revisions: - - 56c31114ad4a - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: picard - owner: devteam - revisions: - - 6f9c0884a3e7 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtools_fastx - owner: iuc - revisions: - - a8d69aee190e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: sra_tools - owner: iuc - revisions: - - aad3885b3216 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastp - owner: iuc - revisions: - - 1d8fe9bc4cb0 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: nanoplot - owner: iuc - revisions: - - 645159bcee2d - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastqc - owner: devteam - revisions: - - e7b2202befea - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: minimap2 - owner: iuc - revisions: - - b3eab4b67562 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: multiqc - owner: iuc - revisions: - - b2f1f75d49c4 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: bwa - owner: devteam - revisions: - - 01ac0a5fedc3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtool_filter2 - owner: devteam - revisions: - - 649a225999a5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: picard - owner: devteam - revisions: - - a1f0b3f4b781 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtools_fastx - owner: iuc - revisions: - - a8d69aee190e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: unicycler - owner: iuc - revisions: - - 23300b42ca18 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: spades - owner: nml - revisions: - - b8c00ce5dfa0 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: bandage - owner: iuc - revisions: - - b2860df42e16 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: ncbi_acc_download - owner: iuc - revisions: - - 1c58de56d587 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: picard - owner: devteam - revisions: - - 6f9c0884a3e7 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: text_processing - owner: bgruening - revisions: - - 0a8c6b61f0f4 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 33151a38533a - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: mafft - owner: rnateam - revisions: - - c5908940967d - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fasttree - owner: iuc - revisions: - - e005e659ae21 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: snpeff - owner: iuc - revisions: - - 74aebe30fb52 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastp - owner: iuc - revisions: - - 1d8fe9bc4cb0 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: bwa - owner: devteam - revisions: - - 01ac0a5fedc3 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: multiqc - owner: iuc - revisions: - - 3d93dd18d9f8 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtool_filter2 - owner: devteam - revisions: - - 649a225999a5 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: samtools_stats - owner: devteam - revisions: - - 145f6d74ff5e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: picard - owner: devteam - revisions: - - a1f0b3f4b781 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: lofreq_viterbi - owner: iuc - revisions: - - cdaab621d454 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: lofreq_call - owner: iuc - revisions: - - 03627f24605f - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: snpsift - owner: iuc - revisions: - - 2b3e65a4252f - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 33151a38533a - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fastp - owner: iuc - revisions: - - 1d8fe9bc4cb0 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: snpeff - owner: iuc - revisions: - - 74aebe30fb52 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: multiqc - owner: iuc - revisions: - - 3d93dd18d9f8 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: bowtie2 - owner: devteam - revisions: - - 749c918495f7 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: picard - owner: devteam - revisions: - - a1f0b3f4b781 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: lofreq_viterbi - owner: iuc - revisions: - - cdaab621d454 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: lofreq_call - owner: iuc - revisions: - - dfadc322b065 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: snpsift - owner: iuc - revisions: - - 2b3e65a4252f - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: collapse_collections - owner: nml - revisions: - - 33151a38533a - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: emboss_5 - owner: devteam - revisions: - - dba489bfcd62 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: mafft - owner: rnateam - revisions: - - c5908940967d - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: emboss_5 - owner: devteam - revisions: - - dba489bfcd62 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: mafft - owner: rnateam - revisions: - - c5908940967d - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: fasttree - owner: iuc - revisions: - - e005e659ae21 - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: hyphy_gard - owner: iuc - revisions: - - 6283babe736e - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: hyphy_absrel - owner: iuc - revisions: - - f73435dc282b - tool_panel_section_label: COVID-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ -- name: sucos_max_score - owner: bgruening - revisions: - - bf99565cec1f - tool_panel_section_label: Covid-19 - tool_shed_url: https://toolshed.g2.bx.psu.edu/ diff --git a/Covid-19-Galaxy-container/Dockerfile b/Covid-19-Galaxy-container/Dockerfile deleted file mode 100644 index 09eef19..0000000 --- a/Covid-19-Galaxy-container/Dockerfile +++ /dev/null @@ -1,24 +0,0 @@ - -# Example Galaxy container -# -# to build the docker image, go to root of training repo and -# docker build -t containername -f Dockerfile . -# -# to run image: -# docker run -p "8080:80" -t containername - -FROM bgruening/galaxy-stable:19.01 -MAINTAINER ELIXIR Belgium - -ENV GALAXY_CONFIG_BRAND "Covid-19" - - -ADD bin/docker-install-workflow.sh /setup-workflow.sh -ADD bin/starter-service.sh /starter-service.sh -#ADD /data /data/ -ADD tools.yaml tools.yaml -ADD /workflow /workflowDir - -RUN /setup-workflow.sh - -ENTRYPOINT ["/starter-service.sh"] \ No newline at end of file diff --git a/Covid-19-Galaxy-container/README.md b/Covid-19-Galaxy-container/README.md deleted file mode 100644 index 8153171..0000000 --- a/Covid-19-Galaxy-container/README.md +++ /dev/null @@ -1,11 +0,0 @@ -# Covid-19 galaxy container - -For more information on the workflows, please check https://github.com/galaxyproject/SARS-CoV-2 - - -``` -docker build -t quay.io/galaxy/covid-19-training -f Dockerfile . -docker run --privileged -p "8080:80" -t quay.io/galaxy/covid-19-training -docker login quay.io -docker push quay.io/galaxy/covid-19-training -``` \ No newline at end of file diff --git a/Covid-19-Galaxy-container/bin/docker-install-workflow.sh b/Covid-19-Galaxy-container/bin/docker-install-workflow.sh deleted file mode 100644 index b7e3572..0000000 --- a/Covid-19-Galaxy-container/bin/docker-install-workflow.sh +++ /dev/null @@ -1,72 +0,0 @@ -#!/bin/bash - -# install everything for workflow to work inside container - -set -e -galaxy_instance="http://localhost:8080" - -# launch the instance -echo "Starting Galaxy..." - -export GALAXY_CONFIG_TOOL_PATH=/galaxy-central/tools/ -startup_lite - -# wait until galaxy has started -galaxy-wait -g $galaxy_instance - -# run install as user galaxy -su - $GALAXY_USER - -# install workflow -echo " - Extracting tools from workflows" -for w in `ls /workflowDir/*.ga | sort -r` -do - echo $w - workflow-to-tools -w $w -o /workflowDir/wftools.yaml -l "Tools from workflows" - echo " - Installing tools from workflow" - n=0 - until [ $n -ge 3 ] - do - shed-tools install -t /workflowDir/wftools.yaml -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD && break - n=$[$n+1] - sleep 5 - echo " - Retrying shed-tools install " - done - echo " - Installing workflow" - workflow-install --publish_workflows --workflow_path $w -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD - -done - -echo "Installing extra tools" -n=0 -until [ $n -ge 3 ] -do - shed-tools install -t tools.yaml -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD && break - n=$[$n+1] - sleep 5 - echo " - Retrying shed-tools install " -done - -echo "Checking for data libraries" -file="/data/data-library.yaml" -if [ -f "$file" ]; -then - if [ "$(head -n 1 $file)" != "{}" ]; - then - setup-data-libraries -i $file -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD -v - echo "Data library installed" - else - echo "No data libraries to install" - fi -else - echo "No data libraries to install" -fi - -# echo "Checking for data managers" -# if [ -f "/data/data-manager.yaml" ] -# then -# echo " - Installing reference data" -# run-data-managers --config "/data/data-manager.yaml" -g $galaxy_instance -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD -# else -# echo " - No reference data to install" -# fi diff --git a/Covid-19-Galaxy-container/bin/starter-service.sh b/Covid-19-Galaxy-container/bin/starter-service.sh deleted file mode 100644 index d2970fb..0000000 --- a/Covid-19-Galaxy-container/bin/starter-service.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash -set -e - -# launch the instance in deamon mode -echo "Starting Galaxy" -startup diff --git a/Covid-19-Galaxy-container/data/data-manager.yaml b/Covid-19-Galaxy-container/data/data-manager.yaml deleted file mode 100644 index 21045f8..0000000 --- a/Covid-19-Galaxy-container/data/data-manager.yaml +++ /dev/null @@ -1,19 +0,0 @@ ---- -# configuration for fetch and index genomes - -data_managers: - # Data manager ID - - id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4 - # tool parameters, nested parameters should be specified using a pipe (|) - params: - - 'dbkey_source|dbkey': '{{ item }}' - - 'reference_source|reference_source_selector': 'ucsc' - - 'reference_source|requested_dbkey': '{{ item }}' - # Items refere to a list of variables you want to run this data manager. You can use them inside the param field with {{ item }} - # In case of genome for example you can run this DM with multiple genomes, or you could give multiple URLs. - items: - - hg38 - # Name of the data-tables you want to reload after your DM are finished. This can be important for subsequent data managers - data_table_reload: - - all_fasta - - __dbkeys__ \ No newline at end of file diff --git a/Covid-19-Galaxy-container/tools.yaml b/Covid-19-Galaxy-container/tools.yaml deleted file mode 100644 index 6f37034..0000000 --- a/Covid-19-Galaxy-container/tools.yaml +++ /dev/null @@ -1,18 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: true -install_tool_dependencies: true -tools: -# - name: data_manager_fetch_genome_dbkeys_all_fasta -# owner: devteam -# revisions: -# - 4d3eff1bc421 -# tool_panel_section_label: Covid-19 -# tool_shed_url: https://toolshed.g2.bx.psu.edu/ - -- name: sucos_max_score - owner: bgruening - revisions: - - bf99565cec1f - tool_panel_section_label: Tools from workflows - tool_shed_url: https://toolshed.g2.bx.psu.edu/ - \ No newline at end of file diff --git a/Covid-19-Galaxy-container/workflow/Cheminformatics-0-XChem_combined.ga b/Covid-19-Galaxy-container/workflow/Cheminformatics-0-XChem_combined.ga deleted file mode 100644 index 95726af..0000000 --- a/Covid-19-Galaxy-container/workflow/Cheminformatics-0-XChem_combined.ga +++ /dev/null @@ -1,1074 +0,0 @@ -{ - 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