Mercurial > repos > pjbriggs > macs21
changeset 7:0c6b14f3fefc draft
Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build.
| author | pjbriggs |
|---|---|
| date | Tue, 21 Apr 2015 08:29:16 -0400 |
| parents | 344dd37d1704 |
| children | 78c15c0a96ae |
| files | macs21_wrapper.py tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 0 deletions(-) [+] |
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--- a/macs21_wrapper.py Tue Apr 21 07:53:37 2015 -0400 +++ b/macs21_wrapper.py Tue Apr 21 08:29:16 2015 -0400 @@ -77,6 +77,10 @@ # Determine genome build chrom_sizes = os.path.basename(chrom_sizes) genome_build = chrom_sizes.split('.')[0] + if genome_build == '?': + # No genome build set + sys.stderr.write("ERROR genome build not set, cannot get sizes for '?'\n") + sys.exit(1) print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build # Run fetchChromSizes chrom_sizes = os.path.join(working_dir,chrom_sizes)
--- a/tool_dependencies.xml Tue Apr 21 07:53:37 2015 -0400 +++ b/tool_dependencies.xml Tue Apr 21 08:29:16 2015 -0400 @@ -32,6 +32,9 @@ <action type="chmod"> <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> </actions> </install> </package>