[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/87b586afb054/ Changeset: 87b586afb054 Branch: stable User: natefoo Date: 2014-01-21 18:39:35 Summary: Add missing requirement tags to converters, fixes Trello #1349. Affected #: 5 files diff -r b2e473cd17cdd0e5758cee32e74f9be7723658bf -r 87b586afb05428a3b0ae37d68c79241994a27021 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml @@ -1,5 +1,8 @@ <tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true"><!-- Used internally to generate track indexes --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs><param format="bedgraph" name="input" type="data" label="Choose wiggle"/> @@ -9,4 +12,4 @@ </outputs><help></help> -</tool> \ No newline at end of file +</tool> diff -r b2e473cd17cdd0e5758cee32e74f9be7723658bf -r 87b586afb05428a3b0ae37d68c79241994a27021 lib/galaxy/datatypes/converters/fasta_to_2bit.xml --- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml @@ -1,6 +1,9 @@ <tool id="CONVERTER_fasta_to_2bit" name="Convert FASTA to 2bit" version="1.0.0"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>faToTwoBit $input $output</command><inputs><param name="input" type="data" format="fasta" label="Fasta file"/> diff -r b2e473cd17cdd0e5758cee32e74f9be7723658bf -r 87b586afb05428a3b0ae37d68c79241994a27021 lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml --- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml @@ -2,6 +2,9 @@ <requirements><requirement type='package'>bowtie</requirement></requirements><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">bowtie</requirement> + </requirements><command> mkdir ${output.files_path} && bowtie-build --quiet diff -r b2e473cd17cdd0e5758cee32e74f9be7723658bf -r 87b586afb05428a3b0ae37d68c79241994a27021 lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml --- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml @@ -2,6 +2,9 @@ <requirements><requirement type='package'>bowtie</requirement></requirements><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">bowtie</requirement> + </requirements><command> mkdir ${output.files_path} && bowtie-build --quiet diff -r b2e473cd17cdd0e5758cee32e74f9be7723658bf -r 87b586afb05428a3b0ae37d68c79241994a27021 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -1,5 +1,8 @@ <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true"><!-- Used internally to generate track indexes --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs><page> @@ -11,4 +14,4 @@ </outputs><help></help> -</tool> \ No newline at end of file +</tool> https://bitbucket.org/galaxy/galaxy-central/commits/8592f010fdc3/ Changeset: 8592f010fdc3 User: natefoo Date: 2014-01-21 18:40:58 Summary: Merge stable. Affected #: 13 files diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml @@ -1,5 +1,8 @@ <tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true"><!-- Used internally to generate track indexes --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs><param format="bedgraph" name="input" type="data" label="Choose wiggle"/> @@ -9,4 +12,4 @@ </outputs><help></help> -</tool> \ No newline at end of file +</tool> diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/datatypes/converters/fasta_to_2bit.xml --- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml @@ -1,6 +1,9 @@ <tool id="CONVERTER_fasta_to_2bit" name="Convert FASTA to 2bit" version="1.0.0"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>faToTwoBit $input $output</command><inputs><param name="input" type="data" format="fasta" label="Fasta file"/> diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml --- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml @@ -2,6 +2,9 @@ <requirements><requirement type='package'>bowtie</requirement></requirements><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">bowtie</requirement> + </requirements><command> mkdir ${output.files_path} && bowtie-build --quiet diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml --- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml +++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml @@ -2,6 +2,9 @@ <requirements><requirement type='package'>bowtie</requirement></requirements><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --><!-- Used on the metadata edit page. --> + <requirements> + <requirement type="package">bowtie</requirement> + </requirements><command> mkdir ${output.files_path} && bowtie-build --quiet diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -1,5 +1,8 @@ <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true"><!-- Used internally to generate track indexes --> + <requirements> + <requirement type="package">ucsc_tools</requirement> + </requirements><command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs><page> @@ -11,4 +14,4 @@ </outputs><help></help> -</tool> \ No newline at end of file +</tool> diff -r df67fd5a8cfc10d269da1ef4b28a184be914badd -r 8592f010fdc345910dc024ec06b68ab2cf2d6642 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -236,6 +236,12 @@ dependency_shell_commands = "&&".join( dependency_shell_commands ) external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + if resolve_requirements: + dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() + if dependency_shell_commands: + if isinstance( dependency_shell_commands, list ): + dependency_shell_commands = "&&".join( dependency_shell_commands ) + external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, env=os.environ, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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