Mercurial > repos > iuc > jbrowse
changeset 28:d0743cb18ed8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
| author | iuc |
|---|---|
| date | Fri, 22 Feb 2019 03:20:59 -0500 |
| parents | 61ce21e36cb5 |
| children | 112eb40ba6cf |
| files | jbrowse.py macros.xml |
| diffstat | 2 files changed, 2 insertions(+), 5 deletions(-) [+] |
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--- a/jbrowse.py Wed Feb 20 11:50:21 2019 -0500 +++ b/jbrowse.py Fri Feb 22 03:20:59 2019 -0500 @@ -614,10 +614,7 @@ if not os.path.exists(dest): # Only index if not already done - cmd = "grep ^\"#\" '%s' > '%s'" % (data, dest) - self.subprocess_popen(cmd) - - cmd = "grep -v ^\"#\" '%s' | grep -v \"^$\" | grep \"\t\" | sort -k1,1 -k4,4n >> '%s'" % (data, dest) + cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest) self.subprocess_popen(cmd) cmd = ['bgzip', '-f', dest]
--- a/macros.xml Wed Feb 20 11:50:21 2019 -0500 +++ b/macros.xml Fri Feb 22 03:20:59 2019 -0500 @@ -14,7 +14,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy1</token> + <token name="@WRAPPER_VERSION@">galaxy2</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution**