annotate tool_dependencies.xml @ 1:0bce36ee6bf2

Edit tpp_gui.pl to change from CGI deprecated endform to end_form
author Jim Johnson <jj@umn.edu>
date Fri, 03 Oct 2014 07:59:16 -0500
parents aad4e1a162c5
children aa519f1dda68
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
2 <tool_dependency>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
3 <package name="libgd" version="2.1.0">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
4 <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
5 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
6 <package name="libpng" version="1.2.5">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
7 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
8 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
9 <package name="bzlib" version="1.0.6">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
10 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
11 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
12 <package name="perl" version="5.18.1">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
13 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
14 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
15 <package name="expat" version="2.1.0">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
16 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
17 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
18 <package name="trans_proteomic_pipeline" version="4.6.3">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
19 <install version="1.0">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
20 <actions>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
21 <!-- populate the environment variables from the dependent repos -->
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
22 <action type="set_environment_for_install">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
23 <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
24 <package name="libgd" version="2.1.0" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
25 </repository>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
26 <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
27 <package name="libpng" version="1.2.5" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
28 </repository>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
29 <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
30 <package name="bzlib" version="1.0.6" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
31 </repository>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
32 <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
33 <package name="expat" version="2.1.0" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
34 </repository>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
35 <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
36 <package name="perl" version="5.18.1" />
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
37 </repository>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
38 </action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
40 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
43
1
0bce36ee6bf2 Edit tpp_gui.pl to change from CGI deprecated endform to end_form
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
44 <!-- Change deprecated CGI endform to end_form -->
0bce36ee6bf2 Edit tpp_gui.pl to change from CGI deprecated endform to end_form
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
45 <action type="shell_command">sed -i.orig 's/endform/end_form/' TPP-4.6.3/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl</action>
0bce36ee6bf2 Edit tpp_gui.pl to change from CGI deprecated endform to end_form
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
46
0
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
47 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
48 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' &gt; Makefile.config.incl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
49 <action type="shell_command">echo 'TPP_WEB=/tpp/' &gt;&gt; Makefile.config.incl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
50 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' &gt;&gt; Makefile.config.incl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
51
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
52 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" &gt; "Makefile.config.incl"</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
53
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
54
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
55 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../CGI/show_nspbin.pl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
56 <action type="shell_command">sed -i -e 's/qw(.*) /(&amp;) /' ../perl/exporTPP.pl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
57 <action type="shell_command">echo '' &gt; ../perl/tpp_models.pl</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
58
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
59 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
60
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
61 <action type="set_environment">
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
62 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
63 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
64 </action>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
65
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
66 </actions>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
67 </install>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
68 <readme>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
69 Installs and compiles the trans proteomic pipeline in version 4.6.3
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
70 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
71
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
72 http://tools.proteomecenter.org/
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
73
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
74 PATH will be set.
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
75 TPP_ROOT_PATH will point to the root path of the installation.
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
76 </readme>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
77 </package>
aad4e1a162c5 Uploaded
iuc
parents:
diff changeset
78 </tool_dependency>