Mercurial > repos > sblanck > package_mpagenomics_1_1_2

changeset 0:bb2877d35401

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Uploaded
author sblanck
date Fri, 24 Apr 2015 05:43:56 -0400
parents
children 37b16e8f2701
files tool_dependencies.xml
diffstat 1 files changed, 67 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Apr 24 05:43:56 2015 -0400
@@ -0,0 +1,67 @@
+<?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>