Mercurial > repos > bgruening > package_samtools_1_0

changeset 0:59273702eab9 draft default tip

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author bgruening
date Fri, 05 Sep 2014 09:58:06 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 61 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Sep 05 09:58:06 2014 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ncurses" version="5.9">
+        <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="zlib" version="1.2.8">
+        <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.19">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                    <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+                <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
+                <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Program: samtools (Tools for alignments in the SAM format)
+Version: 1.0
+
+Usage:   samtools &lt;command&gt; [options]
+
+Command: view        SAM&lt;-&gt;BAM conversion
+         sort        sort alignment file
+         mpileup     multi-way pileup
+         depth       compute the depth
+         faidx       index/extract FASTA
+         tview       text alignment viewer
+         index       index alignment
+         idxstats    BAM index stats (r595 or later)
+         fixmate     fix mate information
+         flagstat    simple stats
+         calmd       recalculate MD/NM tags and '=' bases
+         merge       merge sorted alignments
+         rmdup       remove PCR duplicates
+         reheader    replace BAM header
+         cat         concatenate BAMs
+         targetcut   cut fosmid regions (for fosmid pool only)
+         phase       phase heterozygotes
+
+Requirements: libncurses header files
+        </readme>
+    </package>
+</tool_dependency>