Updated BioSQL wiki page to reflect the latest version #136
Conversation
|
Our automated checks failed, but its an easy thing to fix: |
wiki/BioSQL.md
Outdated
| perform check out (or export) using: | ||
|
|
||
| ```bash | ||
| svn export https://github.com/biopython/biopython/trunk/Tests |
There was a problem hiding this comment.
Please don't recommend using svn here. If you want to avoid needing git, we can just download a tar-ball or zip file from GitHub using e.g.
wget https://github.com/biopython/biopython/archive/biopython-172.zip
unzip biopython-172.zip
Or,
wget https://github.com/biopython/biopython/archive/biopython-172.tar.gz
tar -zxvf biopython-172.tar.gz
Also this lets us recommend getting the tests to match the version of Biopython installed, which should prevent test failures from a version mis-match (although that would be rare with BioSQL as this code is fairly static these days).
| repository at (https://github.com/biosql/biosql.git) | ||
|
|
||
| ``` bash | ||
| svn export https://github.com/biosql/biosql.git/trunk biosql |
There was a problem hiding this comment.
Again, avoid recommending the legacy tool svn here - we want any potential contributors to use git so:
git clone https://github.com/biosql/biosql.git
cd biosqlOr, for a simple snapshot:
wget https://github.com/biosql/biosql/archive/master.tar.gz
tar -zxvf master.tar.gz
cd biosql-master/
| The BioSQL package includes a perl script under | ||
| scripts/load\_ncbi\_taxonomy.pl to download and update the taxonomy | ||
| The BioSQL package includes a perl script under the | ||
| **scripts** subdirectory named **load\_ncbi\_taxonomy.pl** that downloads and updates the taxonomy |
There was a problem hiding this comment.
Use the double back-ticks for file names, load\_ncbi\_taxonomy.pl, rather than double asterisk for bold.
| @@ -92,8 +107,7 @@ mysqladmin -u root create bioseqdb | |||
| ``` | |||
|
|
|||
| We can then tell MySQL to load the BioSQL scheme we downloaded above. | |||
| Change to the scripts subdirectory from the unzipped BioSQL download, | |||
| then: | |||
| Change to the **sql** subdirectory (see above) and then: | |||
There was a problem hiding this comment.
Use the double back-ticks for directory names, sql, rather than the double asterisk for bold.
| @@ -191,8 +205,7 @@ trying to load sequences into the database. This isn't so important with | |||
| Biopython 1.49 onwards, where you can instead opt to have the | |||
| information needed downloaded as needed from Entrez. | |||
|
|
|||
| To update the NCBI taxonomy, change to the scripts subdirectory from the | |||
| unzipped BioSQL download, then: | |||
| To update the NCBI taxonomy, change to the **scripts** subdirectory (see above) and then: | |||
| DBDRIVER = 'MySQLdb' | ||
| DBTYPE = 'mysql' | ||
| ```bash | ||
| svn export https://github.com/biopython/biopython/trunk/Tests |
There was a problem hiding this comment.
Again, please avoid svn export and use git or a plain download from GitHub.
| ``` | ||
|
|
||
| and a little lower down, | ||
| Inside *Tests*, copy the file *biosql.ini.sample* to *biosql.ini* and edit it by filling in the following |
There was a problem hiding this comment.
Use double-backtickes, Tests, biosql.ini.sample and biosql.ini - not single asterisk for italics.
Added cygwin support as well.