Mercurial > repos > joachim-jacob > qualimap_suite
changeset 4:3d690162d629 draft
Added more details for the required dependencies.
| author | Joachim Jacob <joachim.jacob@gmail.com> |
|---|---|
| date | Wed, 20 Mar 2013 09:35:07 +0100 |
| parents | 9537dd9dd18b |
| children | f6ffb9aa409e |
| files | README bamqc.xml bamqc_wrapper.pl |
| diffstat | 3 files changed, 10 insertions(+), 20 deletions(-) [+] |
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--- a/README Tue Feb 12 04:50:47 2013 -0500 +++ b/README Wed Mar 20 09:35:07 2013 +0100 @@ -1,4 +1,4 @@ -qualimap - 1.0.0 +qualimap - 1.0.1 ===================================================================== <joachim.jacob@vib.be> @@ -15,16 +15,19 @@ ----------------------------- Install this tool in your Galaxy via the Toolshed - ) Third party code installation - Required: qualimap JAR archives. + ) Required dependencies: + - Qualimap available in the PATH + - Perl + - Perl core module File::Temp and File::Basename + - Perl module Log::Log4perl ) Integration into Galaxy Please use the toolshed DETAILS AND ISSUES ------------------ - ) Only bamqc provided in this first version - ) bamqc: allow passing number of threads, and take into account number of 'chunks' - ) bamqc: + ) Qualimap suite provide various quality control tools to apply + after mapping. Only bamqc is provided in this first version + ) bamqc reports various statistics of an alignment. =====================================================================
--- a/bamqc.xml Tue Feb 12 04:50:47 2013 -0500 +++ b/bamqc.xml Wed Mar 20 09:35:07 2013 +0100 @@ -1,5 +1,5 @@ -<tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="0.0.1"> +<tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="1.0.1"> <!-- Additional info: wrapper compatible with versions ..... --> <description> to asses mapping quality metrics.
--- a/bamqc_wrapper.pl Tue Feb 12 04:50:47 2013 -0500 +++ b/bamqc_wrapper.pl Wed Mar 20 09:35:07 2013 +0100 @@ -65,19 +65,6 @@ mkdir "$tempdir", 077 unless -d "$tempdir"; INFO "\nTemporary directory:\n$tempdir"; - -# ---------------------- Output files ---------------------------------# -######################################################################## -# Two possible scenarios -# - output is written to the file at the output location in config file -# - output is moved to the output file location - -# open (SAMOUTPUT, ">$para{'output_sam'}") -# or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die ); -# print SAMOUTPUT "Here comes sam\n"; -# close (SAMOUTPUT); - - # -------------------- Assembling command ----------------------------# ######################################################################## my $outdir="bamqc_output";