| Previous changeset 0:6adb6e16b00f (2014-04-02) |
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Commit message:
Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>. |
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modified:
mosaik2.xml readme.rst tool_dependencies.xml |
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| diff -r 6adb6e16b00f -r 1fea05cdc1a1 mosaik2.xml --- a/mosaik2.xml Wed Apr 02 12:32:52 2014 -0400 +++ b/mosaik2.xml Thu Nov 06 13:20:15 2014 -0500 |
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| @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.0.0"> +<tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.2.28.0"> <description/> <requirements> - <requirement type="package" version="2.2.26">mosaik</requirement> + <requirement type="package" version="2.2.28">mosaik</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <version_command>MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p'</version_command> @@ -23,7 +23,7 @@ #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 + MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.78.pe.ann -annse \$MOSAIK_NETWORK_DIR/2.1.78.se.ann $ls_string #if str($mm) -mm $mm #end if @@ -36,7 +36,7 @@ #if str($mhp) -mhp $mhp #end if - -hs 15; + -hs 15 && #if str($outFormat) == 'bam' samtools sort -o mosaik_aligned_file.bam out_prefix > $output #else @@ -141,15 +141,22 @@ .. _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|_. +You can use this tool only if you agree to the license terms of: `MOSAIK`_. .. _MOSAIK: https://code.google.com/p/mosaik-aligner/ + +If you use this tool, please cite: + +- |Cuccuru2014|_ +- |Lee2014|_. + +.. |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* 30(13), 1928-1929 +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 .. |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 </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu135</citation> + <citation type="doi">10.1371/journal.pone.0090581</citation> + </citations> </tool> |
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| diff -r 6adb6e16b00f -r 1fea05cdc1a1 readme.rst --- a/readme.rst Wed Apr 02 12:32:52 2014 -0400 +++ b/readme.rst Thu Nov 06 13:20:15 2014 -0500 |
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| @@ -19,6 +19,7 @@ Version history --------------- +- Release 1: Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>. - Release 0: Initial release in the Tool Shed. Development |
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| diff -r 6adb6e16b00f -r 1fea05cdc1a1 tool_dependencies.xml --- a/tool_dependencies.xml Wed Apr 02 12:32:52 2014 -0400 +++ b/tool_dependencies.xml Thu Nov 06 13:20:15 2014 -0500 |
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| @@ -1,11 +1,20 @@ <?xml version="1.0"?> <tool_dependency> - <package name="mosaik" version="2.2.26"> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="mosaik" version="2.2.28"> <install version="1.0"> <actions> <action type="shell_command">git clone https://github.com/wanpinglee/MOSAIK.git mosaik</action> - <action type="shell_command">git reset --hard e04c806bb1410cf1dbd1534991c46d696aec6723</action> + <action type="shell_command">git reset --hard 24cf066048228a729c79f1de06b403ad8b0bc920</action> <action type="shell_command">sed -i 's/ -static//g' src/includes/linux.inc</action> + <!-- populate the environment variables from the dependent repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> <action type="shell_command">make -C src/</action> <action type="move_directory_files"> <source_directory>bin</source_directory> @@ -16,15 +25,15 @@ <destination_directory>$INSTALL_DIR/networkFile</destination_directory> </action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> <action type="set_environment"> - <environment_variable name="MOSAIK_NETWORK_DIR" action="set_to">$INSTALL_DIR/networkFile</environment_variable> + <environment_variable action="set_to" name="MOSAIK_NETWORK_DIR">$INSTALL_DIR/networkFile</environment_variable> </action> </actions> </install> </package> -<!-- <package name="samtools" version="0.1.19"> - <repository name="package_samtools_0_1_19" owner="devteam" /> - </package>--> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency> |