# HG changeset patch # User peterjc # Date 1431447325 14400 # Node ID 95a5f56a24eb489f5cc6218d1fc1007a3885f3df # Parent 93ef6468b2887d3132e19a9cdef36372b797acb6 planemo upload for https://github.com/peterjc/pico_galaxy/tools/clc_assembly_cell/28b690151fe39a4e66133d37a625d348a1900b5d diff -r 93ef6468b288 -r 95a5f56a24eb tools/clc_assembly_cell/README.rst --- a/tools/clc_assembly_cell/README.rst Fri Nov 21 06:40:45 2014 -0500 +++ b/tools/clc_assembly_cell/README.rst Tue May 12 12:15:25 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_upload --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_upload --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) diff -r 93ef6468b288 -r 95a5f56a24eb tools/clc_assembly_cell/clc_assembler.xml --- a/tools/clc_assembly_cell/clc_assembler.xml Fri Nov 21 06:40:45 2014 -0500 +++ b/tools/clc_assembly_cell/clc_assembler.xml Tue May 12 12:15:25 2015 -0400 @@ -1,8 +1,13 @@ - + Assembles reads giving a FASTA file clc_assembler + + + + + \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version \${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: " - - - - - @@ -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 + + +@MISC{clcbio, +AUTHOR = {CLC Bio} +title ={{CLC Assembly Cell}}, +url = {http://www.clcbio.com/products/clc-assembly-cell/}, +year = {2008--2015} +} + + diff -r 93ef6468b288 -r 95a5f56a24eb tools/clc_assembly_cell/clc_mapper.xml --- a/tools/clc_assembly_cell/clc_mapper.xml Fri Nov 21 06:40:45 2014 -0500 +++ b/tools/clc_assembly_cell/clc_mapper.xml Tue May 12 12:15:25 2015 -0400 @@ -1,4 +1,4 @@ - + Maps reads giving a SAM/BAM file clc_mapper @@ -6,6 +6,11 @@ samtools samtools + + + + + \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version echo Mapping reads with clc_mapper... && \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper @@ -51,11 +56,6 @@ && mv "temp_sorted.bam" "$out_bam" && echo Indexing BAM file with samtools... && samtools index "$out_bam" - - - - - @@ -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 + + +@MISC{clcbio, +AUTHOR = {CLC Bio} +title = {{CLC Assembly Cell}}, +url = {http://www.clcbio.com/products/clc-assembly-cell/}, +year = {2008--2015} +} + + diff -r 93ef6468b288 -r 95a5f56a24eb tools/clc_assembly_cell/tool_dependencies.xml --- a/tools/clc_assembly_cell/tool_dependencies.xml Fri Nov 21 06:40:45 2014 -0500 +++ b/tools/clc_assembly_cell/tool_dependencies.xml Tue May 12 12:15:25 2015 -0400 @@ -1,6 +1,6 @@ - +