Mercurial > repos > yhoogstrate > package_samtools_parallel_mpileup_0_1_19_a

annotate tool_dependencies.xml @ 0:8eea1a2bd1f2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
author yhoogstrate
date Thu, 05 Nov 2015 07:16:56 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
1 <?xml version="1.0"?>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
2 <tool_dependency>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
3 <package name="ncurses" version="6.0">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
4 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
5 </package>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
6
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
7 <package name="samtools_parallel_mpileup" version="0.1.19-a">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
8 <install version="1.0">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
9 <actions>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
10 <action type="set_environment_for_install">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
11 <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
12 <package name="ncurses" version="6.0" />
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
13 </repository>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
14 </action>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
15
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
16 <action type="shell_command">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
17 svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
18
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
19 cd samtools-parallel-mpileup ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
20 cd $(ls |grep samtools-) ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
21
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
22 sed -i 's/-lcurses/-lncurses/' Makefile ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
23 sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
24
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
25 make ;
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
26 cp samtools ../samtools-parallel-mpileup
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
27 </action>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
28 <action type="move_file">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
29 <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
30 <destination>$INSTALL_DIR/bin</destination>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
31 </action>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
32 <action type="set_environment">
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
34 <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
35 </action>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
36 </actions>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
37 </install>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
38 <readme>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
39 Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
40
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
41 *Because of the parallelization, the output is not sorted on genomic location!!*
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
42
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
43 If this is required for the tool that uses the mpileup as input, sort the mpileup file with:
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
44
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
45 sort -k1,1V -k2,2g
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
46 </readme>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
47 </package>
8eea1a2bd1f2 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
48 </tool_dependency>