Mercurial > repos > peterjc > clc_assembly_cell

changeset 1:5ae1c0312aaa draft

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v0.0.3 citation information and internal changes
author peterjc
date Wed, 05 Aug 2015 10:57:39 -0400
parents 0996169ac2e8
children 139b6f0a0bb5
files tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml
diffstat 4 files changed, 74 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- a/tools/clc_assembly_cell/README.rst	Fri Nov 21 06:41:12 2014 -0500
+++ b/tools/clc_assembly_cell/README.rst	Wed Aug 05 10:57:39 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
 ==========================================================
 
-This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -25,8 +25,9 @@
 This wrapper is available from the Galaxy Tool Shed at:
 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 
-This Galaxy wrapper was written and tested using CLC Assembly Cell
-version 4.10.86742
+This Galaxy wrapper was written and tested using CLC Assembly Cell v4.1.0,
+specifically ``clc_assember`` and ``clc_mapper`` binaries for 64 bit Linux
+which report version 4.10.86742 at the command line.
 
 
 Automated Installation
@@ -36,9 +37,16 @@
 install the wrapper from the Galaxy Tool Shed. However, you will need to
 manually install the CLC Assembly Cell software, and setup the environment
 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
-(and in particular, the ``clc_assembler`` binary). For example:
+(in particular, binaries ``clc_assembler``, ``clc_mapper`` and
+``clc_cas_to_sam``). For example::
+
+    $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
 
-$ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
+If your CLC Bio licence is restricted to specific machines on your cluster,
+use Galaxy's job configuration settings to ensure CLC jobs are only sent
+to those licenced computers. For SGE, we use the ``-l hostname="..."``
+option to do this. Alternatively your cluster administrator might setup
+a dedicated job queue.
 
 
 Manual Installation
@@ -49,9 +57,9 @@
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/clcbio/`` folder:
 
-* clc_assembler.xml (Galaxy tool definition)
-* clc_mapper.xml (Galaxy tool definition)
-* README.rst (this file)
+* ``clc_assembler.xml`` (Galaxy tool definition)
+* ``clc_mapper.xml`` (Galaxy tool definition)
+* ``README.rst`` (this file)
 
 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
 the tools. Just all these line, for example next to other assembly tools::
@@ -77,6 +85,9 @@
 v0.0.1  - Initial public release.
 v0.0.2  - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable.
         - Enable and fixed the tests.
+v0.0.3  - Reorder XML elements (internal change only).
+        - Added citation tags.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -86,19 +97,28 @@
 Development is on this itHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    ...
+
+or::
 
-    $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml test-data/NC_010642.fna
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf clcbio.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/clc_assembly_cell/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/NC_010642.fna
     tools/clc_assembly_cell/README.rst
     tools/clc_assembly_cell/clc_assembler.xml
     tools/clc_assembly_cell/clc_mapper.xml
     tools/clc_assembly_cell/tool_dependencies.xml
-    test-data/NC_010642.fna
 
 
 Licence (MIT)
--- a/tools/clc_assembly_cell/clc_assembler.xml	Fri Nov 21 06:41:12 2014 -0500
+++ b/tools/clc_assembly_cell/clc_assembler.xml	Wed Aug 05 10:57:39 2015 -0400
@@ -1,8 +1,13 @@
-<tool id="clc_assembler" name="CLC assembler" version="0.0.2">
+<tool id="clc_assembler" name="CLC assembler" version="0.0.3">
     <description>Assembles reads giving a FASTA file</description>
     <requirements>
         <requirement type="binary">clc_assembler</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
     <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
 #for $rg in $read_group
@@ -27,11 +32,6 @@
 -o "$out_fasta"
 --cpus \${GALAXY_SLOTS:-4}
 -v | grep -v "^Progress: "</command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <repeat name="read_group" title="Read Group" min="1">
             <conditional name="segments">
@@ -127,7 +127,20 @@
 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 
+CLC Assembly Cell, CLC bio (2008--2015)
+http://www.clcbio.com/products/clc-assembly-cell/
+
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
     </help>
+    <citations>
+        <citation type="bibtex">
+@MISC{clcbio,
+AUTHOR = {CLC Bio}
+title ={{CLC Assembly Cell}},
+url = {http://www.clcbio.com/products/clc-assembly-cell/},
+year = {2008--2015}
+}
+        </citation>
+    </citations>
 </tool>
--- a/tools/clc_assembly_cell/clc_mapper.xml	Fri Nov 21 06:41:12 2014 -0500
+++ b/tools/clc_assembly_cell/clc_mapper.xml	Wed Aug 05 10:57:39 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="clc_mapper" name="CLC Mapper" version="0.0.2">
+<tool id="clc_mapper" name="CLC Mapper" version="0.0.3">
     <description>Maps reads giving a SAM/BAM file</description>
     <requirements>
         <requirement type="binary">clc_mapper</requirement>    
@@ -6,6 +6,11 @@
         <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command>
     <command>echo Mapping reads with clc_mapper...
 &amp;&amp; \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
@@ -51,11 +56,6 @@
 &amp;&amp; mv "temp_sorted.bam" "$out_bam"
 &amp;&amp; echo Indexing BAM file with samtools...
 &amp;&amp; samtools index "$out_bam"</command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <!-- Job splitting with merge via clc_join_mappings? -->
     <inputs>
         <!-- Support linear and circular references (-z) -->
@@ -163,7 +163,20 @@
 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
 
+CLC Assembly Cell, CLC bio (2008--2015)
+http://www.clcbio.com/products/clc-assembly-cell/
+
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
     </help>
+    <citations>
+        <citation type="bibtex">
+@MISC{clcbio,
+AUTHOR = {CLC Bio} 
+title = {{CLC Assembly Cell}},
+url = {http://www.clcbio.com/products/clc-assembly-cell/},
+year = {2008--2015}
+}
+        </citation>
+    </citations>
 </tool>
--- a/tools/clc_assembly_cell/tool_dependencies.xml	Fri Nov 21 06:41:12 2014 -0500
+++ b/tools/clc_assembly_cell/tool_dependencies.xml	Wed Aug 05 10:57:39 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>