Mercurial > repos > charles > bismark_upgrade_proposition

changeset 2:2492ef09c164 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author charles
date Mon, 07 Nov 2016 03:47:43 -0500
parents 76faf71cc0b8
children
files bismark/tool_dependencies.xml
diffstat 1 files changed, 0 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- a/bismark/tool_dependencies.xml	Mon Nov 07 03:35:59 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="bowtie2" version="2.1.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie2</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie2-align</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie2-build</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Compiling bowtie2 requires zlib and libpthread to be present on your system.
-        </readme>
-    </package>
-    <package name="bowtie" version="0.12.8">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-inspect</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>bowtie-build</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>