# Galaxy 19.01 drmaa problem switching from galaxy.ini to galaxy.yml

**URL:** <https://help.galaxyproject.org/t/galaxy-19-01-drmaa-problem-switching-from-galaxy-ini-to-galaxy-yml/994>\
**Category:** Uncategorized\
**Tags:** devops-administration\
**Created:** [April 3, 2019, 2:55pm UTC](https://help.galaxyproject.org/t/galaxy-19-01-drmaa-problem-switching-from-galaxy-ini-to-galaxy-yml/994 "2019-04-03T14:55:52Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![bertrand](https://avatars.discourse-cdn.com/v4/letter/b/a88e4f/32.png) [@bertrand](https://help.galaxyproject.org/u/bertrand)\
**Post date:** [April 3, 2019, 2:55pm UTC](https://help.galaxyproject.org/t/galaxy-19-01-drmaa-problem-switching-from-galaxy-ini-to-galaxy-yml/994/1 "2019-04-03T14:55:52Z")

</div>

Hi,

I upgraded our Galaxy instance from 16.xy to 19.01.  
I succeeded to configure it with our deprecated galaxy.ini file.  
But I face problems to migrate configuration to galaxy.yml file and set it up to use our SGE 8.1.8 cluster :

- with galaxy.ini, galaxy jobs are correctly shifted and run by SGE
- but with galaxy.yml, galaxy jobs keep waiting to be shifted but are not received by SGE.

I believe I must have misconfigured something but can’t find what.  
Would you have any hint ?

Here are extracts from :

- our galaxy.yml :

```auto
uwsgi:

  http: :7090
  buffer-size: 16384
  processes: 2
  threads: 4
  offload-threads: 1
  static-map: /static/style=static/style/blue
  static-map: /static=static
  static-map: /favicon.ico=static/favicon.ico
  master: true
  pythonpath: lib
  module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
  thunder-lock: true
  die-on-term: true
  hook-master-start: unix_signal:2 gracefully_kill_them_all
  hook-master-start: unix_signal:15 gracefully_kill_them_all
  py-call-osafterfork: true
  enable-threads: true

galaxy:

  mule: lib/galaxy/main.py
  farm: job-handlers:1

```

- our job\_conf.xml :

```auto
<job_conf>
    <plugins workers="4">
        <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <param id="drmaa_library_path">/SGE/8.1.8/lib/lx-amd64/libdrmaa.so</param>
        </plugin>
    </plugins>
    <destinations default="sge_default">
        <destination id="sge_default" runner="sge">
            <param id="nativeSpecification">-V -j n -q short.q</param>
        </destination>
    </destinations>

```

- our galaxy.log :

```auto
galaxy.jobs.command_factory INFO 2019-04-03 16:42:44,377 [p:14860,w:2,m:0] [DRMAARunner.work_thread-3] Built script [/gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/tool_script.sh] for tool command [python '/gs7k1/home/galaxydev/galaxy_19.01/tools/data_source/upload.py' /gs7k1/home/galaxydev/galaxy_19.01 /gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/registry.xml /gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/upload_params.json 46441:/gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/dataset_46441_files:/gs7k1/home/galaxydev/galaxy_19.01/database/files/046/dataset_46441.dat]
galaxy.jobs.runners DEBUG 2019-04-03 16:42:44,449 [p:14860,w:2,m:0] [DRMAARunner.work_thread-3] (18532) command is: rm -rf working; mkdir -p working; cd working; /gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/tool_script.sh; return_code=$?; cd '/gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532';
galaxy.jobs.runners.drmaa DEBUG 2019-04-03 16:42:44,483 [p:14860,w:2,m:0] [DRMAARunner.work_thread-3] (18532) submitting file /gs7k1/home/galaxydev/galaxy_19.01/database/jobs_directory/018/18532/galaxy_18532.sh
galaxy.jobs.runners.drmaa DEBUG 2019-04-03 16:42:44,483 [p:14860,w:2,m:0] [DRMAARunner.work_thread-3] (18532) native specification is: -V -j n -q short.q

```

Regards.

---

<div class="post-metadata">

**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\
**Post date:** [April 4, 2019, 5:42pm UTC](https://help.galaxyproject.org/t/galaxy-19-01-drmaa-problem-switching-from-galaxy-ini-to-galaxy-yml/994/2 "2019-04-04T17:42:08Z")

</div>

> [@bertrand](#):
>
> mule: lib/galaxy/main.py farm: job-handlers:1

Should be under `uwsgi` section in the config per [Scaling and Load Balancing — Galaxy Project 23.1.1.dev0 documentation](https://docs.galaxyproject.org/en/master/admin/scaling.html#uwsgi-mule-job-handling)

I am not sure that is the root cause but definitely firs thing to try.

---

<div class="post-metadata">

**Author:** ![bertrand](https://avatars.discourse-cdn.com/v4/letter/b/a88e4f/32.png) [@bertrand](https://help.galaxyproject.org/u/bertrand)\
**Post date:** [April 5, 2019, 6:32am UTC](https://help.galaxyproject.org/t/galaxy-19-01-drmaa-problem-switching-from-galaxy-ini-to-galaxy-yml/994/3 "2019-04-05T06:32:15Z")

</div>

Thank you for the hint.

It was in the wrong section. Works fine now.