Mercurial > repos > peterjc > samtools_idxstats
changeset 2:93b8db68dde4 draft
Uploaded v0.0.1b, fixed dependency
| author | peterjc |
|---|---|
| date | Wed, 13 Nov 2013 07:05:15 -0500 |
| parents | 6564815949e0 |
| children | 3070949d8fd7 |
| files | tools/samtools_idxstats/README.rst tools/samtools_idxstats/repository_dependencies.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml |
| diffstat | 4 files changed, 12 insertions(+), 8 deletions(-) [+] |
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--- a/tools/samtools_idxstats/README.rst Mon Nov 11 12:31:47 2013 -0500 +++ b/tools/samtools_idxstats/README.rst Wed Nov 13 07:05:15 2013 -0500 @@ -62,7 +62,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/repository_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular + $ tar -czf samtools_idxstats.tar.gz tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular Check this worked:: @@ -70,7 +70,7 @@ tools/samtools_idxstats/README.rst tools/samtools_idxstats/samtools_idxstats.xml tools/samtools_idxstats/samtools_idxstats.py - tools/samtools_idxstats/repository_dependencies.xml + tools/samtools_idxstats/tool_dependencies.xml test-data/ex1.bam test-data/ex1.idxstats.tabular
--- a/tools/samtools_idxstats/repository_dependencies.xml Mon Nov 11 12:31:47 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the samtools 0.1.19 binaries"> - <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories>
--- a/tools/samtools_idxstats/samtools_idxstats.py Mon Nov 11 12:31:47 2013 -0500 +++ b/tools/samtools_idxstats/samtools_idxstats.py Wed Nov 13 07:05:15 2013 -0500 @@ -32,9 +32,11 @@ bam_filename, bai_filename, tabular_filename = sys.argv[1:] if not os.path.isfile(bam_filename): - stop_err("Input BAM file not found: %s" % bam_filename) + stop_err("Input BAM file not found: %s" % bam_filename) if not os.path.isfile(bai_filename): - stop_err("Input BAI file not found: %s" % bai_filename) + if bai_filename == "None": + stop_err("Error: Galaxy did not index your BAM file") + stop_err("Input BAI file not found: %s" % bai_filename) #Assign sensible names with real extensions, and setup symlinks: tmp_dir = tempfile.mkdtemp()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools_idxstats/tool_dependencies.xml Wed Nov 13 07:05:15 2013 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>