Mercurial > repos > devteam > freebayes

annotate tool_dependencies.xml @ 8:28e422c589ac

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix for FreeBayes tool dependency git checkout commands. Credit goes to Lance Parsons.
author Daniel Blankenberg <dan@bx.psu.edu>
date Wed, 12 Sep 2012 13:06:51 -0400
parents d3bf1e86b243
children d291dc763c4c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
2 <tool_dependency>
5
949ac66308a7 Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 4
diff changeset
3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
4 <install version="1.0">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
5 <actions>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
6 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
8
28e422c589ac Fix for FreeBayes tool dependency git checkout commands. Credit goes to Lance Parsons.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 7
diff changeset
7 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
28e422c589ac Fix for FreeBayes tool dependency git checkout commands. Credit goes to Lance Parsons.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 7
diff changeset
8 <action type="shell_command">git submodule update --recursive</action>
0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
9 <action type="shell_command">make</action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
10 <action type="move_directory_files">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
11 <source_directory>bin</source_directory>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
13 </action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
14 <action type="set_environment">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
16 </action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
17 </actions>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
18 </install>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
19 <readme>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
20 FreeBayes requires g++ and the standard C and C++ development libraries.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
21 Additionally, cmake is required for building the BamTools API.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
22 </readme>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
23 </package>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
24 <package name="samtools" version="0.1.18">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
25 <install version="1.0">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
26 <actions>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
27 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
7
d3bf1e86b243 Make samtools sed command gnu compatible.
Daniel Blankenberg <dan@bx.psu.edu>
parents: 5
diff changeset
28 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
0
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
29 <action type="shell_command">make</action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
30 <action type="move_file">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
31 <source>samtools</source>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
32 <destination>$INSTALL_DIR/bin</destination>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
33 </action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
34 <action type="move_file">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
35 <source>misc/maq2sam-long</source>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
36 <destination>$INSTALL_DIR/bin</destination>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
37 </action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
38 <action type="set_environment">
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
40 </action>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
41 </actions>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
42 </install>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
43 <readme>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
44 Compiling SAMtools requires the ncurses and zlib development libraries.
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
45 </readme>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
46 </package>
61fe907fc37c Uploaded freebayes with tool dependencies
devteam
parents:
diff changeset
47 </tool_dependency>