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comparison mothur/tool_dependencies.xml @ 36:040410b8167e default tip

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Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author galaxyuser <galaxy_user@agr.g.ca>
date Mon, 10 Nov 2014 15:40:02 -0500
parents 95d75b35e4d2
children
comparison
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35:95d75b35e4d2 36:040410b8167e
1 <?eml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <!-- 3 <package name="mothur" version="1.33">
4 <package name="mothur" version="1.27">
5 <install version="1.0"> 4 <install version="1.0">
6 <actions> 5 <actions>
7 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> 6 <action type="download_by_url">http://www.mothur.org/w/images/6/65/Mothur.1.33.3.zip</action>
8 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> 7 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
9 <action type="shell_command"> 8 <action type="shell_command">
10 test $(uname) = Linux &amp;&amp; 9 test $(uname) = Linux &amp;&amp;
11 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile || 10 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile ||
12 true 11 true
13 </action> 12 </action>
14 <action type="shell_command">cd Mothur.source; make -j 2;</action> 13 <action type="shell_command">cd Mothur.source; make -j 2;</action>
15 <action type="move_file"> 14 <action type="move_file">
16 <source>Mothur.source/mothur</source> 15 <source>Mothur.source/mothur</source>
17 <destination>$INSTALL_DIR/bin</destination> 16 <destination>$INSTALL_DIR/bin</destination>
18 </action> 17 </action>
19 <action type="move_file"> 18 <action type="move_file">
20 <source>Mothur.source/uchime</source> 19 <source>Mothur.source/uchime</source>
21 <destination>$INSTALL_DIR/bin</destination> 20 <destination>$INSTALL_DIR/bin</destination>
22 </action> 21 </action>
23 <action type="set_environment"> 22 <action type="set_environment">
24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 23 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
25 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> 24 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
26 </action> 25 </action>
27 </actions> 26 <action type="set_environment_for_install">
28 </install> 27 <repository changeset_revision="8a5a4d8db315" name="package_blast_2_2_26" owner="iyad" toolshed="https://toolshed.g2.bx.psu.edu/">
29 <readme> 28 <package name="blast" version="2.2.26" />
29 </repository>
30 </action>
30 31
31 Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required. libncurses-devel are required. 32 <action type="make_directory">$INSTALL_DIR/bin/blast</action>
33 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
34 <action type="change_directory">$INSTALL_DIR/bin</action>
32 35
33 These links provide information for building the Mothur package in most environments . 36 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
34 37
35 http://www.mothur.org/wiki/Download_mothur 38 </actions>
39 </install>
40 <readme>
41 *Authors &amp; Contacts*
42 Jim Johnson
43 Peter Briggs
44 Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
45 Kevin Chen | Agriculture and Agri-Foods Canada
36 46
37 http://www.mothur.org/wiki/Installation 47 *Description*
38 48
39 http://www.mothur.org/wiki/Makefile_options 49 The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools. In addition, it downloads and builds the Mothur binaries.
40 50
41 </readme> 51 Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
42 </package>
43 -->
44 <package name="mothur" version="1.33">
45 <install version="1.0">
46 <actions>
47 <action type="download_by_url">http://www.mothur.org/w/images/6/65/Mothur.1.33.3.zip</action>
48 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
49 <!--
50 <action type="shell_command">
51 test -e /etc/redhat-release &amp;&amp;
52 perl -i.bak -pe 's/#(CXX.+g\+\+44)/$1/;' Mothur.source/makefile ||
53 true
54 </action>
55 -->
56 <action type="shell_command">
57 test $(uname) = Linux &amp;&amp;
58 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile ||
59 true
60 </action>
61 <action type="shell_command">cd Mothur.source; make -j 2;</action>
62 <action type="move_file">
63 <source>Mothur.source/mothur</source>
64 <destination>$INSTALL_DIR/bin</destination>
65 </action>
66 <action type="move_file">
67 <source>Mothur.source/uchime</source>
68 <destination>$INSTALL_DIR/bin</destination>
69 </action>
70 <action type="set_environment">
71 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
72 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
73 </action>
74 <action type="set_environment_for_install">
75 <repository changeset_revision="32c158152e5e" name="package_blast_plus_2_2_26" owner="meowmeow" toolshed="http://onotta669816x:9001/">
76 <package name="blast" version="2.2.26" />
77 </repository>
78 </action>
79 52
80 <!-- 53 These links provide information for building the Mothur package in most environments.
81 <action type="shell_command">mkdir $INSTALL_DIR/bin/blast; mkdir $INSTALL_DIR/bin/blast/bin;</action>
82 -->
83 <action type="make_directory">$INSTALL_DIR/bin/blast</action>
84 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
85 <action type="change_directory">$INSTALL_DIR/bin</action>
86 <!--
87 <action type="shell_command">cd $INSTALL_DIR/bin; cp ../../../../../../blast/*/*/package_blast_plus_2_2_26/*/* ./blast/bin</action>
88 -->
89 54
90 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action> 55 http://www.mothur.org/wiki/Download_mothur
91 56
92 </actions> 57 http://www.mothur.org/wiki/Installation
93 </install> 58 http://www.mothur.org/wiki/Makefile_options
94 <readme>
95 59
96 Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required. libncurses-devel are required. 60 *Requirements*
97 61
98 These links provide information for building the Mothur package in most environments . 62 - build tools (make, C libraries, GCC)
99 63 - libncurses-dev(el)
100 http://www.mothur.org/wiki/Download_mothur 64 - simplejson (python library)
101 65 </readme>
102 http://www.mothur.org/wiki/Installation 66 </package>
103 67 <package name="blast" version="2.2.26">
104 http://www.mothur.org/wiki/Makefile_options 68 <repository
105 69 name="package_blast_2_2_26"
106 </readme> 70 owner="iyad"
107 </package> 71 changeset_revision="8a5a4d8db315"
108 <!-- 72 toolshed="https://toolshed.g2.bx.psu.edu/"
109 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip 73 prior_installation_required="True"/>
110 --> 74 </package>
111
112 <package name="blast" version="2.2.26">
113 <repository
114 name="package_blast_plus_2_2_26"
115 owner="meowmeow"
116 changeset_revision="32c158152e5e"
117 toolshed="http://onotta669816x:9001/"
118 prior_installation_required="True"/>
119 </package>
120 75
121 </tool_dependency> 76 </tool_dependency>
122 77