| Previous changeset 0:cb87eae7fc3e (2013-08-19) Next changeset 2:b471600c8a3b (2014-04-27) |
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Commit message:
Also install bcftools and misc utility commands when installing samtools. |
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modified:
tool_dependencies.xml |
| b |
| diff -r cb87eae7fc3e -r 00e17a794a2e tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 19 17:19:38 2013 -0400 +++ b/tool_dependencies.xml Tue Sep 17 11:36:59 2013 -0500 |
| b |
| @@ -6,10 +6,25 @@ <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> <action type="shell_command">make</action> + <action type="shell_command">chmod ugo+rx misc/*.p?</action> + <action type="shell_command">mkdir misc/bin</action> + <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> + <action type="move_file"> + <source>bcftools/bcftools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/vcfutils.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_directory_files"> + <source_directory>misc/bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> @@ -38,6 +53,29 @@ cat concatenate BAMs targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes + +This also installs bcftools and misc utility commands: + bcftools + vcfutils.pl + ace2sam + bamcheck + blast2sam.pl + bowtie2sam.pl + export2sam.pl + interpolate_sam.pl + maq2sam-long + maq2sam-short + md5fa + md5sum-lite + novo2sam.pl + psl2sam.pl + sam2vcf.pl + samtools.pl + soap2sam.pl + varfilter.py + wgsim + wgsim_eval.pl + zoom2sam.pl </readme> </package> </tool_dependency> |