Mercurial > repos > iuc > package_stacks_1_40

diff tool_dependencies.xml @ 0:f413df160b3e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:23:58 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Jun 25 17:23:58 2016 -0400
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="stacks" version="1.40">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks_1.40_src_all.tar.gz</action>
+
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="samtools" version="0.1.19" />
+                    </repository>
+                </action>
+
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_INCLUDE} --with-bam-lib-path=${BAM_LIB_PATH}</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <!-- create env.sh -->
+                <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
+                        <environment_variable action="set_to" name="STACKS_ROOT_DIR">$INSTALL_DIR/</environment_variable>
+                </action>
+           </actions>
+        </install>
+        <readme>
+            This package installs STACKS from the sources available. Based on Cyril Monjeuad version
+        </readme>
+    </package>
+</tool_dependency>