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