Mercurial > repos > pjbriggs > pal_finder
annotate tool_dependencies.xml @ 6:a73c48890bde draft
Version v0.02.04.5: handle large output files
author | pjbriggs |
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date | Tue, 06 Jun 2017 08:54:49 -0400 |
parents | b6ccc7dd7b02 |
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rev | line source |
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0 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
3 <package name="pal_finder" version="0.02.04"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz</action> | |
7 <action type="move_file"> | |
8 <source>pal_finder_v0.02.04.pl</source> | |
9 <destination>$INSTALL_DIR/bin</destination> | |
10 </action> | |
11 <action type="move_file"> | |
12 <source>config.txt</source> | |
13 <destination>$INSTALL_DIR/data</destination> | |
14 </action> | |
15 <action type="move_file"> | |
16 <source>simple.ref</source> | |
17 <destination>$INSTALL_DIR/data</destination> | |
18 </action> | |
19 <action type="set_environment"> | |
20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
21 </action> | |
22 <action type="set_environment"> | |
23 <environment_variable name="PALFINDER_SCRIPT_DIR" action="set_to">$INSTALL_DIR/bin</environment_variable> | |
24 </action> | |
25 <action type="set_environment"> | |
26 <environment_variable name="PALFINDER_DATA_DIR" action="set_to">$INSTALL_DIR/data</environment_variable> | |
27 </action> | |
28 </actions> | |
29 </install> | |
30 <readme>pal_finder also needs Perl</readme> | |
31 </package> | |
1
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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32 <package name="perl" version="5.16.3"> |
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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33 <install version="1.0"> |
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34 <actions> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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35 <!-- install perl --> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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36 <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz</action> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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37 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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38 <action type="make_install" /> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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39 <action type="set_environment"> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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41 </action> |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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42 </actions> |
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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43 </install> |
771ebe02636f
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44 <readme> |
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45 Perl 5 is a highly capable, feature-rich programming language with over 25 years of |
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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46 development: |
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47 |
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48 http://www.perl.org/ |
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49 </readme> |
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50 </package> |
0 | 51 <package name="primer3_core" version="2.0.0"> |
52 <install version="1.0"> | |
53 <actions> | |
54 <action type="download_by_url">https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz</action> | |
55 <action type="shell_command">make -C src -f Makefile</action> | |
56 <action type="move_file"> | |
57 <source>src/primer3_core</source> | |
58 <destination>$INSTALL_DIR/bin</destination> | |
59 </action> | |
60 <action type="set_environment"> | |
61 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
62 </action> | |
63 </actions> | |
64 </install> | |
65 <readme>primer3_core</readme> | |
66 </package> | |
2 | 67 <package name="biopython" version="1.65"> |
68 <install version="1.0"> | |
69 <actions> | |
70 <action type="shell_command">pip install --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action> | |
71 <action type="set_environment"> | |
72 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable> | |
73 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable> | |
74 </action> | |
75 </actions> | |
76 </install> | |
77 <readme>BioPython 1.65</readme> | |
78 </package> | |
79 <package name="pandaseq" version="2.8.1"> | |
80 <install version="1.0"> | |
81 <actions> | |
82 <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action> | |
83 <action type="shell_command">./autogen.sh</action> | |
84 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> | |
85 <action type="shell_command">make</action> | |
86 <action type="shell_command">make install</action> | |
87 <action type="set_environment"> | |
88 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
89 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> | |
90 </action> | |
91 </actions> | |
92 </install> | |
93 <readme>PANDASeq 2.8.1 | |
94 | |
95 PANDASEQ is a program to align Illumina reads, optionally | |
96 with PCR primers embedded in the sequence, and reconstruct | |
97 an overlapping sequence. | |
98 | |
99 https://github.com/neufeld/pandaseq | |
100 </readme> | |
101 </package> | |
0 | 102 </tool_dependency> |