Mercurial > repos > iuc > package_mothur_1_36_1

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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
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-1:000000000000 0:c4cbfb49f1b6
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="mothur" version="1.36.1">
4 <install version="1.0">
5 <actions>
6 <action sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22" type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
7 <action type="set_environment_for_install">
8 <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
9 <package name="legacy_blast" version="2.2.22" />
10 </repository>
11 <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
12 <package name="boost" version="1.57" />
13 </repository>
14 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
15 <package name="zlib" version="1.2.8" />
16 </repository>
17 </action>
18 <action type="shell_command">chmod u+x source/uchime_src/mk</action>
19 <action type="shell_command">
20 test $(uname) = Linux &amp;&amp;
21 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
22 true
23 </action>
24 <action type="shell_command">sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile;</action>
25 <action type="shell_command">sed -i.bak -e '141d;151d;152d' source/makefile;</action>
26 <action type="shell_command">sed -i.bak -e 's/fortranSource//g' source/makefile;</action>
27 <action type="shell_command">sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
28 <action type="shell_command">sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>
29
30 <action type="shell_command">cd source; make -j 2;</action>
31 <action type="move_file">
32 <source>mothur</source>
33 <destination>$INSTALL_DIR/bin</destination>
34 </action>
35 <action type="move_file">
36 <source>source/uchime</source>
37 <destination>$INSTALL_DIR/bin</destination>
38 </action>
39 <action type="set_environment">
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
41 </action>
42 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
43 <action type="change_directory">$INSTALL_DIR/bin</action>
44 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
45 </actions>
46 </install>
47 <readme>
48 *Authors &amp; Contacts*
49 Jim Johnson
50 Peter Briggs
51 Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
52 Kevin Chen | Agriculture and Agri-Foods Canada
53
54 *Description*
55
56 The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools. In addition, it downloads and builds the Mothur binaries.
57
58 Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
59
60 These links provide information for building the Mothur package in most environments.
61
62 http://www.mothur.org/wiki/Download_mothur
63
64 http://www.mothur.org/wiki/Installation
65 http://www.mothur.org/wiki/Makefile_options
66
67 *Requirements*
68
69 - build tools (make, C libraries, GCC)
70 - libncurses-dev(el)
71 - simplejson (python library)
72 </readme>
73 </package>
74 <package name="legacy_blast" version="2.2.22">
75 <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
76 </package>
77 <package name="boost" version="1.57">
78 <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
79 </package>
80 <package name="zlib" version="1.2.8">
81 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
82 </package>
83 </tool_dependency>