diff tools/clc_assembly_cell/README.rst @ 1:5ae1c0312aaa draft

v0.0.3 citation information and internal changes

--- 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)