Mercurial > repos > iuc > package_mothur_1_36_1

changeset 0:c4cbfb49f1b6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
author iuc
date Mon, 01 Aug 2016 14:34:05 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 83 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 01 14:34:05 2016 -0400
@@ -0,0 +1,83 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="mothur" version="1.36.1">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22" type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="legacy_blast" version="2.2.22" />
+                    </repository>
+                    <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="boost" version="1.57" />
+                    </repository>
+                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+                <action type="shell_command">chmod u+x source/uchime_src/mk</action>
+                <action type="shell_command">
+                    test $(uname) = Linux &amp;&amp;
+                    perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
+                    true
+                </action>
+                <action type="shell_command">sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile;</action>
+                <action type="shell_command">sed -i.bak -e '141d;151d;152d' source/makefile;</action>
+                <action type="shell_command">sed -i.bak -e 's/fortranSource//g' source/makefile;</action>
+                <action type="shell_command">sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
+                <action type="shell_command">sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>
+
+                <action type="shell_command">cd source; make -j 2;</action>
+                <action type="move_file">
+                    <source>mothur</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>source/uchime</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
+                <action type="change_directory">$INSTALL_DIR/bin</action>
+                <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
+            </actions>
+        </install>
+        <readme>
+*Authors &amp; Contacts*
+Jim Johnson
+Peter Briggs
+Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
+Kevin Chen | Agriculture and Agri-Foods Canada
+
+*Description*
+
+The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools.  In addition, it downloads and builds the Mothur binaries.
+
+Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
+
+These links provide information for building the Mothur package in most environments.
+
+http://www.mothur.org/wiki/Download_mothur
+
+http://www.mothur.org/wiki/Installation
+http://www.mothur.org/wiki/Makefile_options
+
+*Requirements*
+
+- build tools (make, C libraries, GCC)
+- libncurses-dev(el)
+- simplejson (python library)
+        </readme>
+    </package>
+    <package name="legacy_blast" version="2.2.22">
+        <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="boost" version="1.57">
+        <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="zlib" version="1.2.8">
+        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>