Mercurial > repos > yhoogstrate > package_samtools_parallel_mpileup_0_1_19_a

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
author yhoogstrate
date Thu, 05 Nov 2015 07:48:42 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ncurses" version="6.0">
4 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6
7 <package name="samtools_parallel_mpileup" version="0.1.19-a">
8 <install version="1.0">
9 <actions>
10 <action type="set_environment_for_install">
11 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
12 <package name="ncurses" version="6.0" />
13 </repository>
14 </action>
15
16 <action type="shell_command">
17 svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
18
19 cd samtools-parallel-mpileup ;
20 cd $(ls |grep samtools-) ;
21
22 sed -i 's/-lcurses/-lncurses/' Makefile ;
23 sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
24
25 make ;
26 cp samtools ../samtools-parallel-mpileup
27 </action>
28 <action type="move_file">
29 <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
30 <destination>$INSTALL_DIR/bin</destination>
31 </action>
32 <action type="set_environment">
33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
34 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
35 </action>
36 </actions>
37 </install>
38 <readme>
39 Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
40
41 *Because of the parallelization, the output is not sorted on genomic location!!*
42
43 If this is required for the tool that uses the mpileup as input, sort the mpileup file with:
44
45 sort -k1,1V -k2,2g
46 </readme>
47 </package>
48 </tool_dependency>