Commit b3bae515 authored by Aaron Petkau's avatar Aaron Petkau

Changed command for generating workflow template and fixed up freebayes tool dependencies

parent 61ec80ee
......@@ -143,7 +143,7 @@ Updating Workflow
If you wish to update the workflow, the template file can be generated with a command like:
```bash
sed -e 's/"[^"]*core_pipeline/"[% LOCAL_REPOSITORY %]\/core_pipeline/' -e 's/"[^"]*smalt_collection/"[% LOCAL_REPOSITORY %]\/smalt_collection/' -e 's/"[^"]*phyml/"[% LOCAL_REPOSITORY %]\/phyml/' -e 's/"[^"]*freebayes/"[% LOCAL_REPOSITORY %]\/freebayes/' path/to/Galaxy-Workflow-Core_SNP_Pipeline.ga > workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt
$ perl -pe 's/"[^"]+?core_pipeline\//"[% LOCAL_REPOSITORY %]\/core_pipeline\//; s/"[^"]+?smalt_collection\//"[% LOCAL_REPOSITORY %]\/smalt_collection\//; s/"[^"]+?phyml\//"[% LOCAL_REPOSITORY %]\/phyml\//; s/"[^"]+?freebayes\//"[% LOCAL_REPOSITORY %]\/freebayes\//' path/to/Galaxy-Workflow-Core_SNP_Pipeline.ga > workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt
```
[Core Phylogenomis Pipeline]: https://github.com/apetkau/core-phylogenomics
......
<?xml version="1.0"?>
<tool_dependency>
<package name="freebayes" version="0.9.9_296a0fad5b73377e0c4498c65d53ad743225d6b9"/>
<package name="freebayes" version="0.9.9_296a0fad5b73377e0c4498c65d53ad743225d6b9">
<install version="1.0">
<actions>
<action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
<action type="shell_command">git checkout 296a0fad5b73377e0c4498c65d53ad743225d6b9</action>
<action type="shell_command">git submodule update --recursive</action>
<action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
<action type="move_directory_files">
<source_directory>bin</source_directory>
<destination_directory>$INSTALL_DIR/bin</destination_directory>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</install>
<readme>
FreeBayes requires g++ and the standard C and C++ development libraries.
Additionally, cmake is required for building the BamTools API.
</readme>
</package>
</tool_dependency>
<?xml version="1.0"?>
<tool_dependency>
<package name="freebayes" version="0.9.9_296a0fad5b73377e0c4498c65d53ad743225d6b9">
<install version="1.0">
<actions>
<action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
<action type="shell_command">git checkout 296a0fad5b73377e0c4498c65d53ad743225d6b9</action>
<action type="shell_command">git submodule update --recursive</action>
<action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
<action type="move_directory_files">
<source_directory>bin</source_directory>
<destination_directory>$INSTALL_DIR/bin</destination_directory>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</install>
<readme>
FreeBayes requires g++ and the standard C and C++ development libraries.
Additionally, cmake is required for building the BamTools API.
</readme>
</package>
</tool_dependency>
......@@ -254,7 +254,7 @@
},
"post_job_actions": {},
"tool_errors": null,
"tool_id": "[% LOCAL_REPOSITORY %]/freebayes/0.0.4",
"tool_id": "[% LOCAL_REPOSITORY %]/freebayes/freebayes/0.0.4",
"tool_state": "{\"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"section_mappability_priors_expectations_type\\\": {\\\"section_mappability_priors_expectations_type_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 0}, \\\"haplotype_basis_alleles\\\": null, \\\"output_trace_option\\\": \\\"False\\\", \\\"dont_left_align_indels\\\": \\\"False\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"input_variant_type\\\": {\\\"input_variant_type_selector\\\": \\\"do_not_provide\\\", \\\"__current_case__\\\": 0}, \\\"report_all_haplotype_alleles\\\": \\\"False\\\", \\\"section_algorithmic_features_type\\\": {\\\"exclude_unobserved_genotypes\\\": \\\"False\\\", \\\"genotyping_max_iterations\\\": \\\"1000\\\", \\\"report_genotype_likelihood_max\\\": \\\"False\\\", \\\"genotype_variant_threshold\\\": \\\"\\\", \\\"posterior_integration_limits_m\\\": \\\"3\\\", \\\"posterior_integration_limits_n\\\": \\\"1\\\", \\\"harmonic_indel_quality\\\": \\\"False\\\", \\\"section_algorithmic_features_type_selector\\\": \\\"set\\\", \\\"site_selection_max_iterations\\\": \\\"5\\\", \\\"read_dependence_factor\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"use_mapping_quality\\\": \\\"False\\\", \\\"genotyping_max_banddepth\\\": \\\"7\\\", \\\"genotype_qualities\\\": \\\"False\\\"}, \\\"input_populations_file\\\": null, \\\"section_reporting_type\\\": {\\\"section_reporting_type_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 0}, \\\"section_population_priors_type\\\": {\\\"section_population_priors_type_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 0}, \\\"section_allele_scope_type\\\": {\\\"section_allele_scope_type_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 0}, \\\"section_input_filters_type\\\": {\\\"min_alternate_count\\\": \\\"2\\\", \\\"section_input_filters_type_selector\\\": \\\"set\\\", \\\"__current_case__\\\": 1, \\\"min_coverage\\\": \\\"20\\\", \\\"mismatch_base_quality_threshold\\\": \\\"10\\\", \\\"read_snp_limit\\\": \\\"\\\", \\\"quality_filter_type\\\": {\\\"min_supporting_allele_qsum\\\": \\\"0\\\", \\\"min_base_quality\\\": \\\"30\\\", \\\"min_mapping_quality\\\": \\\"30\\\", \\\"quality_filter_type_selector\\\": \\\"apply_filters\\\", \\\"__current_case__\\\": 1, \\\"min_supporting_mapping_qsum\\\": \\\"0\\\"}, \\\"read_max_mismatch_fraction\\\": \\\"1.0\\\", \\\"min_alternate_fraction\\\": \\\"0.75\\\", \\\"read_indel_limit\\\": \\\"\\\", \\\"use_duplicate_reads\\\": \\\"False\\\", \\\"min_alternate_total\\\": \\\"1\\\", \\\"read_mismatch_limit\\\": \\\"\\\", \\\"indel_exclusion_window\\\": \\\"-1\\\", \\\"min_alternate_qsum\\\": \\\"0\\\"}, \\\"__current_case__\\\": 1, \\\"section_population_model_type\\\": {\\\"section_population_model_type_selector\\\": \\\"set\\\", \\\"pooled_continuous\\\": \\\"False\\\", \\\"pooled_discrete\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"theta\\\": \\\"0.001\\\", \\\"ploidy\\\": \\\"1\\\"}, \\\"use_reference_allele_type\\\": {\\\"use_reference_allele_type_selector\\\": \\\"do_not_include_reference_allele\\\", \\\"__current_case__\\\": 0}, \\\"output_failed_alleles_option\\\": \\\"False\\\", \\\"target_limit_type\\\": {\\\"target_limit_type_selector\\\": \\\"do_not_limit\\\", \\\"__current_case__\\\": 0}, \\\"input_cnv_map_bed\\\": null, \\\"input_sample_file\\\": null}\", \"__page__\": 0}",
"tool_version": "0.0.4",
"type": "tool",
......@@ -322,7 +322,7 @@
"annotation": "",
"id": 10,
"input_connections": {
"[% LOCAL_REPOSITORY %]/freebayes_collection": {
"freebayes_collection": {
"id": 9,
"output_name": "vcfout"
},
......@@ -373,7 +373,7 @@
},
"tool_errors": null,
"tool_id": "[% LOCAL_REPOSITORY %]/core_pipeline/vcf2pseudoalignment/0.0.9",
"tool_state": "{\"ambiguous\": \"\\\"False\\\"\", \"reference\": \"\\\"Reference\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"invalid\": \"null\", \"coverage\": \"\\\"20\\\"\", \"[% LOCAL_REPOSITORY %]/freebayes_collection\": \"null\", \"numcpus\": \"\\\"32\\\"\", \"mpileup_collection\": \"null\"}",
"tool_state": "{\"ambiguous\": \"\\\"False\\\"\", \"reference\": \"\\\"Reference\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"invalid\": \"null\", \"coverage\": \"\\\"20\\\"\", \"freebayes_collection\": \"null\", \"numcpus\": \"\\\"32\\\"\", \"mpileup_collection\": \"null\"}",
"tool_version": "0.0.9",
"type": "tool",
"user_outputs": []
......@@ -413,7 +413,7 @@
}
},
"tool_errors": null,
"tool_id": "[% LOCAL_REPOSITORY %]/phyml1/3.1",
"tool_id": "[% LOCAL_REPOSITORY %]/phyml/phyml1/3.1",
"tool_state": "{\"prop_invar\": \"\\\"0.0\\\"\", \"search\": \"\\\"NNI\\\"\", \"__page__\": 0, \"gamma_condition\": \"{\\\"shape\\\": \\\"e\\\", \\\"categories\\\": \\\"4\\\", \\\"gamma\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}\", \"support_condition\": \"{\\\"support\\\": \\\"sh\\\", \\\"__current_case__\\\": 0}\", \"random_condition\": \"{\\\"random\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"datatype_condition\": \"{\\\"tstv\\\": \\\"e\\\", \\\"model\\\": \\\"HKY85\\\", \\\"type\\\": \\\"nt\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"__rerun_remap_job_id__\": null}",
"tool_version": "3.1",
"type": "tool",
......
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