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Merge branch 'release_18.01' into release_18.05

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Nicola Soranzo
2018-06-17 12:05:50 +01:00
parent a2ff5efbce 3707fb4eb1
commit e8beea0d60
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@@ -146,31 +146,15 @@ Runs jobs via the [TORQUE Resource Manager](http://www.adaptivecomputing.com/pro
#### Dependencies
Galaxy uses the [pbs_python](https://oss.trac.surfsara.nl/pbs_python/) module to interface with TORQUE. pbs_python must be compiled against your TORQUE installation, so it cannot be provided with Galaxy. However, we provide all the necessary automation to compile it - ([more about Galaxy's Framework dependencies](framework_dependencies.html)):
Galaxy uses the [pbs_python](https://github.com/ehiggs/pbs-python) module to interface with TORQUE. pbs_python must be compiled against your TORQUE installation, so it cannot be provided with Galaxy. You can install the package as follows:
```console
galaxy_user@galaxy_server% cd /clusterfs/galaxy/galaxy-app
galaxy_user@galaxy_server% LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python
galaxy_user@galaxy_server% git clone https://github.com/ehiggs/pbs-python
galaxy_user@galaxy_server% cd pbs-python
galaxy_user@galaxy_server% source /clusterfs/galaxy/galaxy-app/.venv/bin/activate
galaxy_user@galaxy_server% python setup.py install
```
#### Newer versions of TORQUE (>4.2)
Galaxy is compatible with newer versions of TORQUE now that pbs_python has been updated to add support for TORQUE >= v4.2. Scrambling the new version of pbs_python is accomplished simply by modifying eggs.ini to use the new version of pbs_python:
```ini
;pbs_python = 4.3.5
pbs_python = 4.4.0
```
Then scramble as normal:
```console
galaxy_user@galaxy_server% cd /clusterfs/galaxy/galaxy-app
galaxy_user@galaxy_server% LIBTORQUE_DIR=/path/to/libtorque python scripts/scramble.py -e pbs_python
```
As of May 2014 there are still some outstanding bugs in pbs_python. Notably, error code translation is out of alignment. For example if you get error #15025 "Bad UID for Job Execution" pbs_python will report this error incorrectly as "Queue already exists". You may consult the [TORQUE source code](https://github.com/adaptivecomputing/torque/blob/4.2.7/src/include/pbs_error_db.h) for the proper error message that corresponds with a given error number.