changeset 1:ccadfae70b02 draft

Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.

--- a/COPYING	Tue Oct 15 11:15:28 2013 -0400
+++ b/COPYING	Wed Mar 05 06:48:08 2014 -0500
@@ -1,4 +1,4 @@
-Copyright © 2013 CRS4 Srl. http://www.crs4.it/
+Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
 Created by:
 Andrea Pinna <[e-mail]>
 Nicola Soranzo <[e-mail]>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Wed Mar 05 06:48:08 2014 -0500
@@ -0,0 +1,28 @@
+SEQuel wrapper
+==============
+
+Configuration
+-------------
+
+sequel_wrapper tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
+
+If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
+
+If instead you are using an older Galaxy release, you should also add a line
+
+  GALAXY_SLOTS=N; export GALAXY_SLOTS
+
+(where N is the number of CPU cores allocated by the job runner for this tool) to the file
+
+  <tool_dependencies_dir>/sequel/1.0.2/crs4/sequel/<hash_string>/env.sh
+
+Version history
+---------------
+
+- Release 1: Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
+- Release 0: Initial release in the Tool Shed.
+
+Development
+-----------
+
+Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!

--- a/sequel_wrapper.xml	Tue Oct 15 11:15:28 2013 -0400
+++ b/sequel_wrapper.xml	Wed Mar 05 06:48:08 2014 -0500
@@ -6,8 +6,7 @@
     <requirement type="package" version="1.0.2">sequel</requirement>
   </requirements>
   <command interpreter="python">
-    sequel_wrapper.py
-    \${SEQUEL_SITE_OPTIONS:--t 8 -p 8 -u 1}
+    sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1
     --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs
     #if str($bases_length)
       --bases_length=$bases_length
@@ -78,11 +77,11 @@
 
     <param name="min_aln_score" type="integer" value="1" optional="true" label="Min alignment score (MAPQ) of reads to consider (-q)" help="" />
 
-    <param name="single_cell_mode" type="boolean" optional="true" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" />
+    <param name="single_cell_mode" type="boolean" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" />
 
-    <param name="report_changes" type="boolean" optional="true" checked="false" label="Report changes (slow) for all input-contigs (-r)" />
+    <param name="report_changes" type="boolean" checked="false" label="Report changes (slow) for all input-contigs (-r)" />
 
-    <param name="extend_contig" type="boolean" optional="true" checked="false" label="Extend contig with flanking regions of alignment (-e)" />
+    <param name="extend_contig" type="boolean" checked="false" label="Extend contig with flanking regions of alignment (-e)" />
 
     <param name="reference_genome" type="data" format="fasta,twobit" optional="true" label="Evaluate refinement using reference genome (-g)" help="FASTA or 2bit format" />
   </inputs>
@@ -120,7 +119,7 @@
 
 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
 
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
+.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
 .. _Cuccuru2013: http://orione.crs4.it/
 
 This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_.

--- a/tool_dependencies.xml	Tue Oct 15 11:15:28 2013 -0400
+++ b/tool_dependencies.xml	Wed Mar 05 06:48:08 2014 -0500
@@ -4,7 +4,7 @@
     <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="blat" version="35">
-<!--    <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
+    <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="sequel" version="1.0.2">
     <install version="1.0">
@@ -20,13 +20,10 @@
         <action type="set_environment">
           <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
         </action>
-        <action type="set_environment">
-          <environment_variable action="set_to" name="SEQUEL_SITE_OPTIONS">"-t 8 -p 8 -u 1"</environment_variable>
-        </action>
       </actions>
     </install>
     <readme>
-Change the SEQUEL_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u).
+Configuration: Previously (until Release 0), the SEQUEL_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>