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Updated BioSQL wiki page to reflect the latest version #136

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eefb2b3
Add cygwin instructions
leptoceratops Sep 20, 2018
190dcb7
forgot parenthesis
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65ce8e3
sql not scripts
leptoceratops Sep 20, 2018
c8e57f6
Update BioSQL.md
leptoceratops Sep 20, 2018
43de72b
added description of relevant files
leptoceratops Sep 20, 2018
d7e6acb
correct small typo "scripts"
leptoceratops Sep 20, 2018
bde029a
added more details about running the perl script
leptoceratops Sep 20, 2018
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some more package details
leptoceratops Sep 20, 2018
af4272c
better English
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remove "as well" typo
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better English
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added "so"
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biosql.ini.sample instructions
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inside biosql.ini
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_mysql_connector
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76 changes: 45 additions & 31 deletions wiki/BioSQL.md
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Original file line number Diff line number Diff line change
Expand Up @@ -46,38 +46,53 @@ Installing Required Software
You will need to install some database software plus the associated
python library so that Biopython can "talk" to the database. In this
example we'll talk about the most common choice, MySQL. How you do this
will also depend on your operating system, for example on a Debian or
Ubuntu Linux machine try this:
will also depend on your operating system.
For example on a **Debian or Ubuntu Linux** machine try this:

``` bash
sudo apt-get install mysql-common mysql-server python-mysqldb
```

It will also be important to have perl (to run some of the setup
scripts). Again, on a Debian or Ubuntu Linux machine try this:
scripts). Again, on a **Debian or Ubuntu Linux** machine try this:

``` bash
sudo apt-get install perl
```

You may find perl is already installed.

For Windows users, see [BioSQL on Windows](BioSQL_Windows "wikilink").
For **Windows** users, see [BioSQL on Windows](BioSQL_Windows "wikilink").

For **Cygwin** users, use [apt-cyg](https://github.com/transcode-open/apt-cyg) to install packages **mysql** and **mysql-server**,
``` bash
apt-cyg install mysql mysql-server
```
and to install the driver **mysql-connector** use [pip](https://pypi.org/project/pip/),

``` bash
pip install mysql-connector
```

Downloading the BioSQL Schema & Scripts
---------------------------------------

Once the software is installed, your next task is to setup a database
and import the BioSQL schema (i.e. setup the relevant tables within the
database). See [BioSQL downloads](http://www.biosql.org/wiki/Downloads)
Once the software is installed, your next task is to setup a database,
import the BioSQL schema (i.e. setup the relevant tables within the
database) and finally populate the database.

In order to do so, files from the **biosql** project need to be obtained:

* Either from [BioSQL downloads](http://www.biosql.org/wiki/Downloads)
-- you'll need to unzip the archive.

Alternatively to get the very latest BioSQL, check out their git
repository. Or, navigate to the relevant schema file for your database
and download just that, e.g.
[biosqldb-mysql.sql](https://raw.github.com/biosql/biosql/master/sql/biosqldb-mysql.sql)
for MySQL. You will also want the NCBI Taxonomy loading perl script,
[load\_ncbi\_taxonomy.pl](https://raw.github.com/biosql/biosql/master/scripts/load_ncbi_taxonomy.pl).
* Or to get the **very latest** files, check out (or export) the relevant git
repository at (https://github.com/biosql/biosql.git)

``` bash
svn export https://github.com/biosql/biosql.git/trunk biosql
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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 biosql

Or, for a simple snapshot:

wget https://github.com/biosql/biosql/archive/master.tar.gz
tar -zxvf master.tar.gz
cd biosql-master/

```
The names of the two files that are needed are the following:
1. biosqldb-mysql.sql -- the BioSQL schema -- found inside the **sql** subdirectory
2. load_ncbi_taxonomy.pl -- the Perl script to populate the database -- found inside the **scripts** subdirectory

Creating the empty database
---------------------------
Expand All @@ -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:
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Use the double back-ticks for directory names, sql, rather than the double asterisk for bold.


``` bash
mysql -u root bioseqdb < biosqldb-mysql.sql
Expand Down Expand Up @@ -176,11 +190,11 @@ psql biosqldb < biosqldb-pg.sql

Run *psql* and type enter *\\d <ENTER>* to see all the entities created.

NCBI Taxonomy
-------------
Populate the database With NCBI Taxonomy
----------------------------------------

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
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Use the double back-ticks for file names, load\_ncbi\_taxonomy.pl, rather than double asterisk for bold.

tables. The script should be able to download the files it needs from
the [NCBI taxonomy FTP site](ftp://ftp.ncbi.nih.gov/pub/taxonomy/)
automatically.
Expand All @@ -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:
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scripts


``` bash
./load_ncbi_taxonomy.pl --dbname bioseqdb --driver mysql --dbuser root --download true
Expand Down Expand Up @@ -248,19 +261,20 @@ Running the unit tests
----------------------

Because there are so many ways you could have setup your BioSQL
database, you have to tell the unit test a few bits of information by
editing the file Tests/setup\_BioSQL.py and filling in the following
database, you have to tell the unit test a few bits of information.
If you installed biopython using pip then the relevant [**Tests**](https://github.com/biopython/biopython/tree/master/Tests)
folder would not have been copied. If this is the case one can
perform check out (or export) using:

```bash
svn export https://github.com/biopython/biopython/trunk/Tests
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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).

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Again, please avoid svn export and use git or a plain download from GitHub.

```
Inside *Tests*, copy the file *biosql.ini.sample* to *biosql.ini* and edit it by filling in the following
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Use double-backtickes, Tests, biosql.ini.sample and biosql.ini - not single asterisk for italics.

fields:

``` python
DBDRIVER = 'MySQLdb'
DBTYPE = 'mysql'
```

and a little lower down,

``` python
DBHOST = 'localhost'
DBUSER = 'root'
DBPASSWD = ''
TESTDB = 'biosql_test'
Expand Down