| Previous changeset 40:17359b808b01 (2020-08-21) Next changeset 42:6cd09d7b5f37 (2021-02-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38" |
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modified:
jbrowse-fromdir.xml jbrowse.py jbrowse.xml macros.xml readme.rst |
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| diff -r 17359b808b01 -r 8774b28235bb jbrowse-fromdir.xml --- a/jbrowse-fromdir.xml Fri Aug 21 04:42:41 2020 -0400 +++ b/jbrowse-fromdir.xml Thu Dec 31 16:00:42 2020 +0000 |
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| @@ -3,6 +3,13 @@ <macros> <import>macros.xml</import> </macros> + <edam_operations> + <edam_operation>operation_3434</edam_operation> + </edam_operations> + <edam_topics> + <edam_topic>topic_3307</edam_topic> + <edam_topic>topic_0092</edam_topic> + </edam_topics> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ## Create output directory |
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| diff -r 17359b808b01 -r 8774b28235bb jbrowse.py --- a/jbrowse.py Fri Aug 21 04:42:41 2020 -0400 +++ b/jbrowse.py Thu Dec 31 16:00:42 2020 +0000 |
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| @@ -400,6 +400,14 @@ def _jbrowse_bin(self, command): return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) + def symlink_or_copy(self, src, dest): + if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']): + cmd = ['ln', '-s', src, dest] + else: + cmd = ['cp', src, dest] + + return self.subprocess_check_call(cmd) + def process_genomes(self): for genome_node in self.genome_paths: # We only expect one input genome per run. This for loop is just @@ -507,8 +515,7 @@ def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): dest = os.path.join('data', 'raw', trackData['label'] + '.bw') - cmd = ['cp', data, dest] - self.subprocess_check_call(cmd) + self.symlink_or_copy(os.path.realpath(data), dest) url = os.path.join('raw', trackData['label'] + '.bw') trackData.update({ @@ -535,8 +542,7 @@ urls = [] for idx, bw in enumerate(data): dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw') - cmd = ['ln', '-s', bw[1], dest] - self.subprocess_check_call(cmd) + self.symlink_or_copy(bw[1], dest) urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]}) @@ -598,11 +604,8 @@ def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): dest = os.path.join('data', 'raw', trackData['label'] + '.bam') - cmd = ['ln', '-s', os.path.realpath(data), dest] - self.subprocess_check_call(cmd) - - cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] - self.subprocess_check_call(cmd) + self.symlink_or_copy(os.path.realpath(data), dest) + self.symlink_or_copy(os.path.realpath(bam_index), dest + '.bai') url = os.path.join('raw', trackData['label'] + '.bam') trackData.update({ |
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| diff -r 17359b808b01 -r 8774b28235bb jbrowse.xml --- a/jbrowse.xml Fri Aug 21 04:42:41 2020 -0400 +++ b/jbrowse.xml Thu Dec 31 16:00:42 2020 +0000 |
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| @@ -3,7 +3,18 @@ <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">jbrowse</xref> + </xrefs> <expand macro="requirements"/> + <edam_operations> + <edam_operation>operation_0573</edam_operation> + <edam_operation>operation_0564</edam_operation> + </edam_operations> + <edam_topics> + <edam_topic>topic_3307</edam_topic> + <edam_topic>topic_0092</edam_topic> + </edam_topics> <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> <command detect_errors="aggressive"><![CDATA[ #if $action.action_select == "create": @@ -667,7 +678,6 @@ </outputs> <tests> <test> - <!-- gencode --> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> <param name="gencode" value="1" /> |
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| diff -r 17359b808b01 -r 8774b28235bb macros.xml --- a/macros.xml Fri Aug 21 04:42:41 2020 -0400 +++ b/macros.xml Thu Dec 31 16:00:42 2020 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.16.9</token> + <token name="@TOOL_VERSION@">1.16.10</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement> |
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| diff -r 17359b808b01 -r 8774b28235bb readme.rst --- a/readme.rst Fri Aug 21 04:42:41 2020 -0400 +++ b/readme.rst Thu Dec 31 16:00:42 2020 +0000 |
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| @@ -25,6 +25,15 @@ History ======= +- 1.16.10+galaxy0 + + - UPDATED to JBrowse 1.16.10 + - ADDED GALAXY_JBROWSE_SYMLINKS environment variable: if set, the tool will make symlinks to bam/bigwig files instead of copying them + +- 1.16.9+galaxy0 + + - UPDATED to JBrowse 1.16.9 + - 1.16.8+galaxy0 - UPDATED to JBrowse 1.16.8 |