Mercurial > repos > sblanck > package_mpagenomics_1_1_2

changeset 1:37b16e8f2701

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Deleted selected files
author sblanck
date Fri, 24 Apr 2015 05:45:00 -0400
parents bb2877d35401
children 3d8d46bafceb
files tool_dependencies.xml
diffstat 1 files changed, 0 insertions(+), 67 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Apr 24 05:43:56 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-
-    <package name="R" version="3.1.2">
-
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="http://localhost:9009" />
-
-    </package>
-
-
-    <package name="mpagenomics" version="1.1.2">
-
-        <install version="1.0">
-
-            <actions>
-
-                <action type="set_environment_for_install">
-
-                    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="http://localhost:9009">
-
-                        <package name="R" version="3.1.2" />
-
-                    </repository>
-
-                </action>
-
-
-                <!--action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/DNAcopy_1.42.0.tar.gz</action>
-                <action type="download_file">http://cran.r-project.org/src/contrib/MPAgenomics_1.1.2.tar.gz</action>
-   				<action type="download_file">http://www.braju.com/R/repos/sfit_0.3.0.tar.gz</action>
-   				<action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/affxparser_1.40.0.tar.gz</action>
-               
-                <action type="download_file">http://www.bioconductor.org/packages/release/bioc/src/contrib/aroma.light_2.4.0.tar.gz</action>
-                
-                <action type="download_file">http://cran.r-project.org/src/contrib/aroma.affymetrix_2.13.0.tar.gz</action>
-                <action type="download_file">http://cran.r-project.org/src/contrib/aroma.cn_1.6.0.tar.gz</action-->
-   				<action type="make_directory">$INSTALL_DIR/mpagenomics/</action>
-
-                <action type="shell_command">
-
-                    export PATH=$PATH:$R_HOME/bin &amp;&amp; 
-
-                    export R_LIBS=$INSTALL_DIR/mpagenomics/ &amp;&amp; 
-
-                	Rscript -e "source('http://www.braju.com/R/hbLite.R')" -e "hbLite('sfit')" -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite('affxparser')"  -e "biocLite('DNAcopy')" -e "biocLite('aroma.light')" -e "install.packages(c('aroma.affymetrix','aroma.cn'),lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)"  -e "install.packages('MPAgenomics',lib='$INSTALL_DIR/mpagenomics/', repos='http://cran.us.r-project.org', dependencies=TRUE)"                 
-                </action>
-                <action type="set_environment">
-
-                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/mpagenomics/</environment_variable>
-
-                </action>
-
-            </actions>
-
-        </install>
-
-        <readme>
-
-        mpagenomics
-
-        Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
-
-        </readme>
-
-    </package>
-
-</tool_dependency>