Mercurial > repos > eganrol > deseq2biomart

changeset 0:ae1154667341 draft default tip

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author eganrol
date Thu, 20 Nov 2014 08:03:01 -0500
parents
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files package_DESeq2/tool_dependencies.xml
diffstat 1 files changed, 63 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package_DESeq2/tool_dependencies.xml	Thu Nov 20 08:03:01 2014 -0500
@@ -0,0 +1,63 @@
+<?xml version="1.0"?>
+<tool_dependency>
+<package name="R_3_0_2" version="3.0.2">
+	<repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu"/>
+</package>
+    <package name="deseq2" version="1.6.2">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+							<repository changeset_revision="b6fe8ca3230d" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu">
+                        <package name="R_3_0_2" version="3.0.2" />
+                    </repository>
+                </action>
+
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/AnnotationDbi_1.28.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/Biobase_2.26.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/BiocGenerics_0.10.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/BiocParallel_1.0.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/BiocStyle_1.5.3.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/DBI_0.3.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/DESeq2_1.6.2.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/DESeq_1.18.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/GenomicRanges_1.18.3.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/Hmisc_3.14-5.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/IRanges_2.0.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/R.methodsS3_1.6.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/RColorBrewer_1.0-5.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/RSQLite_1.0.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/RUnit_0.4.27.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/Rcpp_0.11.3.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/S4Vectors_0.4.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/XML_3.98-1.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/airway_0.99.5.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/annotate_1.44.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/biomaRt_2.22.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/ggplot2_1.0.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/gplots_2.14.2.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/knitr_1.8.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/locfit_1.5-9.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/pasilla_0.5.1.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/rjson_0.2.15.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/vsn_3.34.0.tar.gz</action>
+                <action type="download_file">ftp://ftp-igbmc/pub/slegras/R/xtable_1.7-4.tar.gz</action>
+                
+
+                <action type="make_directory">$INSTALL_DIR/deseq2/</action>
+                <action type="shell_command">
+                    export PATH=$PATH:$R_HOME/bin &amp;&amp; 
+                    export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp; 
+                    Rscript -e "install.packages(c('AnnotationDbi_1.28.1.tar.gz','Biobase_2.26.0.tar.gz','BiocGenerics_0.10.0.tar.gz','BiocParallel_1.0.0.tar.gz','BiocStyle_1.5.3.tar.gz','DBI_0.3.1.tar.gz','DESeq2_1.6.2.tar.gz','DESeq_1.18.0.tar.gz','GenomicRanges_1.18.3.tar.gz','Hmisc_3.14-5.tar.gz','IRanges_2.0.0.tar.gz','R.methodsS3_1.6.1.tar.gz','RColorBrewer_1.0-5.tar.gz','RSQLite_1.0.0.tar.gz','RUnit_0.4.27.tar.gz','Rcpp_0.11.3.tar.gz','S4Vectors_0.4.0.tar.gz','XML_3.98-1.1.tar.gz','airway_0.99.5.tar.gz','annotate_1.44.0.tar.gz','biomaRt_2.22.0.tar.gz','ggplot2_1.0.0.tar.gz','gplots_2.14.2.tar.gz','knitr_1.8.tar.gz','locfit_1.5-9.1.tar.gz','pasilla_0.5.1.tar.gz','rjson_0.2.15.tar.gz','vsn_3.34.0.tar.gz','xtable_1.7-4.tar.gz'),lib='$INSTALL_DIR/deseq2/', repos=NULL, dependencies=FALSE)"
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        Differential gene expression analysis based on the negative binomial distribution.
+        http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
+        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>