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comparison orthologs/ucsb_hamster/README_UCSBhamster @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 Dependancies that must be installed and available in path:
2 blastall
3 formatdb
4
5 Dependancies distributed with hamster and galaxy hamster
6 BioPerl
7 genewise
8 rungenewise.pm
9 wisecfg -- directory of configuration files for genewise
10
11
12
13 QUICKSTART
14
15 1. Copy galaxy_hamster files into the directory where you want to
16 install the program.
17
18 2. execute the install.pl script to configure required directories.
19 Type:
20
21 ./install.pl
22
23 3. Make sure blastall and formatdb are installed on your system,
24 and have been configured on your PATH.
25
26 4. add ucsb_hamster.xml to Galaxy's tool_conf.xml file.
27
28 5. Restart Galaxy
29
30
31 Now, ucsb hamster can be used using HMM's constructed in a Galaxy
32 history using phytab_hmmbuild.
33
34
35
36
37
38
39 DETAILED INSTALLATION PROCEDURES:
40
41 If for some reason install.pl does not work, first make sure that
42 you have deleted the PATH variable pointing to any existing galaxy_hamster
43 installation on your system in the .bashrc file.
44
45 If you have deleted this variable and still cannot execute the install script,
46 you may follow the detailed installation procedure below.
47
48 1. Copy galaxy_hamster files into the directory where you want to install
49 the program.
50
51 2. Directory that contains the following scripts must be in the overall
52 path:
53 translate.pl
54 emap2fasta.pl
55 unbuild.py
56
57 You may add the directory into your .bashrc file located in your HOME directory.
58
59 For example:
60 export PATH="/home/galaxy/galaxy-dist/tools/galaxy_hamster:$PATH";
61
62 3. Type: source .bashrc to reload your environment variables.
63
64 4. In the file run_genewise.pm located in the lib direcotry, you must set the full
65 path of the genewise configuration directory. The configurat iondirectory is
66 called wisecfg and it is distributed with galaxy_hamster.
67
68 5. From here, ensure that blastall and formatdb are installed on your system and
69 have been configured on your PATH.
70
71 6. Add ucsb_hamster.xml to Galaxy's tool_conf.xml file.
72
73 7. When installing on an Ubuntu system, the ucsb_hamster.sh script was not finding
74 translate.pl even though it was in the path. To fix this I (THO) added translate.pl and
75 the main hamster script to /usr/local/bin/ with a symbolic link, which seemed to fix
76 this problem.
77
78 8. Restart Galaxy.