Mercurial > repos > nick > dunovo

comparison tool_dependencies.xml @ 11:0f8e0dc73d1d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
author nick
date Wed, 16 Feb 2022 22:59:00 +0000
parents 9dc43bf7d1db
children
comparison
equal deleted inserted replaced
10:9dc43bf7d1db 11:0f8e0dc73d1d
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="bowtie" version="1.1.2">
4 <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="mafft" version="7.221">
7 <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="networkx" version="1.10">
10 <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="dunovo" version="2.15">
13 <install version="1.0">
14 <actions>
15 <!-- download the main dunovo package files -->
16 <action sha256sum="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.tar.gz</action>
17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
18 <!-- install submodules -->
19 <action type="shell_command">rmdir kalign utillib ET</action>
20 <!-- download the utillib submodule -->
21 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
22 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
23 <action type="shell_command">rm v0.1.0.tar.gz</action>
24 <action rename_to="utillib" type="move_file">
25 <source>utillib-0.1.0</source>
26 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
27 </action>
28 <!-- download the kalign submodule -->
29 <action type="download_file">https://github.com/makovalab-psu/kalign-dunovo/archive/v0.2.0.tar.gz</action>
30 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
31 <action type="shell_command">rm v0.2.0.tar.gz</action>
32 <action rename_to="kalign" type="move_file">
33 <source>kalign-dunovo-0.2.0</source>
34 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
35 </action>
36 <!-- download the ET submodule -->
37 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
38 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
39 <action type="shell_command">rm v0.2.2.tar.gz</action>
40 <action rename_to="ET" type="move_file">
41 <source>ET-0.2.2</source>
42 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
43 </action>
44 <!-- download the bfx submodule -->
45 <action type="download_file">https://github.com/NickSto/bfx/archive/v0.2.0.tar.gz</action>
46 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
47 <action type="shell_command">rm v0.2.0.tar.gz</action>
48 <action rename_to="bfx" type="move_file">
49 <source>bfx-0.2.0</source>
50 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
51 </action>
52 <!-- Move some source files from subdirectories into the main source directory. -->
53 <action type="move_file">
54 <source>utils/precheck.py</source>
55 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
56 </action>
57 <action type="move_file">
58 <source>bfx/trimmer.py</source>
59 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
60 </action>
61 <action type="move_file">
62 <source>utils/getreads.py</source>
63 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
64 </action>
65 <!-- make and install -->
66 <action type="shell_command">make clean</action>
67 <action type="shell_command">make</action>
68 <action type="move_directory_files">
69 <source_directory>.</source_directory>
70 <destination_directory>$INSTALL_DIR</destination_directory>
71 </action>
72 <action type="set_environment">
73 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
74 </action>
75 </actions>
76 </install>
77 </package>
78 </tool_dependency>