Mercurial > repos > mzytnicki > s_mart
changeset 112:c181ca344322 draft
Uploaded
| author | mzytnicki |
|---|---|
| date | Wed, 24 Apr 2013 06:24:45 -0400 |
| parents | 1409d4dbf17e |
| children | 15bcd04d07be |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 2 insertions(+), 14 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Apr 24 06:23:03 2013 -0400 +++ b/tool_dependencies.xml Wed Apr 24 06:24:45 2013 -0400 @@ -6,20 +6,8 @@ <package name="samtools" version="0.1.12"> <install version="1.0"> <actions> - <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/tool_shed_dependencies/bamedit/samtoolspkg.tar</action> - <action type="shell_command">chmod ago+x samtools</action> - <action type="shell_command">chmod ago+x maq2sam-long</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> + <action type="shell_command">R --slave --no-save --no-restore --quiet -e 'if (!require("RColorBrewer")){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'</action> + <action type="shell_command">R --slave --no-save --no-restore --quiet -e 'if (!require("Hmisc")){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'</action> </actions> </install> <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>