# HG changeset patch # User crs4 # Date 1396456372 14400 # Node ID 6adb6e16b00fb12966f1e012e1612d356ca021d4 Uploaded diff -r 000000000000 -r 6adb6e16b00f COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,179 @@ +Copyright (c) 2005-2013 Pennsylvania State University +Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ +Created by: +Dannon Baker +Nicola Soranzo + +Licensed under the Academic Free License version 3.0 + + 1) Grant of Copyright License. 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However, You may modify the text of this License and copy, + distribute or communicate your modified version (the "Modified + License") and apply it to other original works of authorship subject to + the following conditions: (i) You may not indicate in any way that your + Modified License is the "Academic Free License" or "AFL" and you may not + use those names in the name of your Modified License; (ii) You must + replace the notice specified in the first paragraph above with the + notice "Licensed under " or with a notice + of your own that is not confusingly similar to the notice in this + License; and (iii) You may not claim that your original works are open + source software unless your Modified License has been approved by Open + Source Initiative (OSI) and You comply with its license review and + certification process. diff -r 000000000000 -r 6adb6e16b00f mosaik2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mosaik2.xml Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,155 @@ + + + + + mosaik + samtools + + MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p' + + MosaikBuild -fr + #if $genomeSource.refGenomeSource == 'indexed' + ${genomeSource.indexReference.fields.path} + #else + ${genomeSource.historyReference} + #end if + -oa mosaik_ref_file; + MosaikBuild -q $reads + #if $paired.kind == 'single' + #set $ls_string = '' + #else + -q2 ${paired.reads2} + -mfl ${paired.mfl} + #set $ls_string = '-ls %s' % $paired.ls + #end if + -st $st -out mosaik_reads_file; + MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.26.pe.100.0065.ann -annse \$MOSAIK_NETWORK_DIR/2.1.26.se.100.005.ann $ls_string + #if str($mm) + -mm $mm + #end if + #if str($act) + -act $act + #end if + #if str($bw) + -bw $bw + #end if + #if str($mhp) + -mhp $mhp + #end if + -hs 15; + #if str($outFormat) == 'bam' + samtools sort -o mosaik_aligned_file.bam out_prefix > $output + #else + samtools view mosaik_aligned_file.bam -o $output + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool uses `MOSAIK`_ v. 2 to align reads to a reference sequence. + +**License and citation** + +This Galaxy tool is Copyright © 2005-2013 Pennsylvania State University, © 2013-2014 `CRS4 Srl.`_ and is released under the `Academic Free License v. 3.0`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0 + +If you use this tool in Galaxy, please cite |Cuccuru2014|_. + +.. |Cuccuru2014| 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 +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135 + +This tool uses `MOSAIK`_, which is licensed separately. Please cite |Lee2014|_. + +.. _MOSAIK: https://code.google.com/p/mosaik-aligner/ +.. |Lee2014| replace:: Lee, W.-P., *et al.* (2014) MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. *PLoS ONE* 9(3), e90581 +.. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581 + + diff -r 000000000000 -r 6adb6e16b00f readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,27 @@ +MOSAIK v.2 wrapper +================== + +Configuration +------------- + +mosaik2 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 + + /mosaik/2.2.26/crs4/mosaik2//env.sh + +Version history +--------------- + +- 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! diff -r 000000000000 -r 6adb6e16b00f tool-data/mosaik_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mosaik_index.loc.sample Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,19 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Mosaik indexed sequences data files. You will need +#to create these data files and then create a mosaik_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The mosaik_index.loc +#file has this format (longer white space is the TAB character): +# +# +# +#So, for example, if you had hg18 indexed and stored in +#/depot/data2/galaxy/mosaik/hg18/ +#then the mosaik_index.loc entry would look like this: +# +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +# +#and your /depot/data2/galaxy/mosaik/hg18/ directory +#would contain the following files: +#TODO handle mosaik jump tables. +# diff -r 000000000000 -r 6adb6e16b00f tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 6adb6e16b00f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 02 12:32:52 2014 -0400 @@ -0,0 +1,30 @@ + + + + + + git clone https://github.com/wanpinglee/MOSAIK.git mosaik + git reset --hard e04c806bb1410cf1dbd1534991c46d696aec6723 + sed -i 's/ -static//g' src/includes/linux.inc + make -C src/ + + bin + $INSTALL_DIR/bin + + + src/networkFile + $INSTALL_DIR/networkFile + + + $INSTALL_DIR/bin + + + $INSTALL_DIR/networkFile + + + + + +