Mercurial > repos > jjohnson > mothur_toolsuite

comparison mothur/tool_dependencies.xml @ 35:95d75b35e4d2

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents 1be61ceb20d7
children 040410b8167e
comparison
equal deleted inserted replaced
34:1be61ceb20d7 35:95d75b35e4d2
1 <?xml version="1.0"?> 1 <?eml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="mothur" version="1.27"> 3 <!--
4 <install version="1.0"> 4 <package name="mothur" version="1.27">
5 <actions> 5 <install version="1.0">
6 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> 6 <actions>
7 <!-- Update the makefile --> 7 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action>
8 <action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action> 8 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
9 <action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action> 9 <action type="shell_command">
10 <action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action> 10 test $(uname) = Linux &amp;&amp;
11 <!-- Update the uchime_src/mk --> 11 perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' Mothur.source/makefile ||
12 <action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</action> 12 true
13 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> 13 </action>
14 <action type="shell_command">cd Mothur.source &amp;&amp; make</action> 14 <action type="shell_command">cd Mothur.source; make -j 2;</action>
15 <action type="move_file"> 15 <action type="move_file">
16 <source>Mothur.source/mothur</source> 16 <source>Mothur.source/mothur</source>
17 <destination>$INSTALL_DIR/bin</destination> 17 <destination>$INSTALL_DIR/bin</destination>
18 </action> 18 </action>
19 <action type="move_file"> 19 <action type="move_file">
20 <source>Mothur.source/uchime</source> 20 <source>Mothur.source/uchime</source>
21 <destination>$INSTALL_DIR/bin</destination> 21 <destination>$INSTALL_DIR/bin</destination>
22 </action> 22 </action>
23 <action type="set_environment"> 23 <action type="set_environment">
24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 24 <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> 25 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
26 </action> 26 </action>
27 </actions> 27 </actions>
28 </install> 28 </install>
29 <readme> 29 <readme>
30 These links provide information for building the Mothur package in most environments .
31 30
32 http://www.mothur.org/wiki/Download_mothur 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.
33 32
34 http://www.mothur.org/wiki/Installation 33 These links provide information for building the Mothur package in most environments .
35 34
36 http://www.mothur.org/wiki/Makefile_options 35 http://www.mothur.org/wiki/Download_mothur
37 36
38 </readme> 37 http://www.mothur.org/wiki/Installation
39 </package>
40 <!--
41 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
42 -->
43 </tool_dependency>
44 38
39 http://www.mothur.org/wiki/Makefile_options
40
41 </readme>
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
80 <!--
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
90 <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
91
92 </actions>
93 </install>
94 <readme>
95
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.
97
98 These links provide information for building the Mothur package in most environments .
99
100 http://www.mothur.org/wiki/Download_mothur
101
102 http://www.mothur.org/wiki/Installation
103
104 http://www.mothur.org/wiki/Makefile_options
105
106 </readme>
107 </package>
108 <!--
109 http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
110 -->
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
121 </tool_dependency>
122