Mercurial > repos > devteam > freebayes
annotate tool_dependencies.xml @ 9:d291dc763c4c
Add an optional alternative make route for compiling FreeBayes; solves issues seen installing under certain architectures.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Wed, 05 Jun 2013 15:00:03 -0400 |
| parents | 28e422c589ac |
| children | 07d55d9ea9a4 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
|
5
949ac66308a7
Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
4
diff
changeset
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3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf"> |
| 0 | 4 <install version="1.0"> |
| 5 <actions> | |
| 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
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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> |
|
9
d291dc763c4c
Add an optional alternative make route for compiling FreeBayes; solves issues seen installing under certain architectures.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
8
diff
changeset
|
9 <action type="shell_command">make || ( make clean && sed -i.bak -e 's:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g' src/Makefile && make )</action> |
| 0 | 10 <action type="move_directory_files"> |
| 11 <source_directory>bin</source_directory> | |
| 12 <destination_directory>$INSTALL_DIR/bin</destination_directory> | |
| 13 </action> | |
| 14 <action type="set_environment"> | |
| 15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 16 </action> | |
| 17 </actions> | |
| 18 </install> | |
| 19 <readme> | |
| 20 FreeBayes requires g++ and the standard C and C++ development libraries. | |
| 21 Additionally, cmake is required for building the BamTools API. | |
| 22 </readme> | |
| 23 </package> | |
| 24 <package name="samtools" version="0.1.18"> | |
| 25 <install version="1.0"> | |
| 26 <actions> | |
| 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
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28 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> |
| 0 | 29 <action type="shell_command">make</action> |
| 30 <action type="move_file"> | |
| 31 <source>samtools</source> | |
| 32 <destination>$INSTALL_DIR/bin</destination> | |
| 33 </action> | |
| 34 <action type="move_file"> | |
| 35 <source>misc/maq2sam-long</source> | |
| 36 <destination>$INSTALL_DIR/bin</destination> | |
| 37 </action> | |
| 38 <action type="set_environment"> | |
| 39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 40 </action> | |
| 41 </actions> | |
| 42 </install> | |
| 43 <readme> | |
| 44 Compiling SAMtools requires the ncurses and zlib development libraries. | |
| 45 </readme> | |
| 46 </package> | |
| 47 </tool_dependency> |