Anthony Bretaudeau

formatdb and mgblast dependencies

4

Hi, @cmonjeau and me are trying to make a bioconda recipe for transposome, but we are stuck on a strange dependency on formatdb and mgblast. It looks like at some...

Pass destination env vars and tags when resubmitting jobs

4

While playing with the sorting hat, I've noticed that some env vars I had set for specific tools where not passed when jobs were resubmitted. This PR fixes this problem...

bcftools install

1

While working on https://github.com/galaxyproject/ansible-galaxy-extras/pull/224 I've notice this little problem: - start a new 18.09 galaxy container (all-in-one image) - don't run any tool, or do anything - run a script...

iprscan5 not up to date on MTS

1

¡Hola! I just realised the [interproscan5 repo on MTS](https://toolshed.g2.bx.psu.edu/repository?repository_id=3e00b72eb27a2633) is not up to date with the xml in https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5, probably because the tool is in the .tt_skip list Would it...

Deadlocks when testing ImageJ tools

6

A strange problem: when testing with planemo some imagej tools (https://github.com/bgruening/galaxytools/blob/master/tools/image_processing/imagej2/imagej2_create_image.xml for example), the test never ends. When doing a `ps` the ImageJ process is in T state (=stopped) and...

Error with postgresql 12

13

I tried to run a new apollo with a postgres 12.1 container, but got this error at startup: ``` apollo_1 | 2019-12-09 11:07:59,154 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate - HHH000388: Unsuccessful: alter...

Plugin loading without setup.sh

19

Hi, In recent JBrowse version (1.15.x, 1.16), to add a plugin we have to run setup.sh to rebuild all the js stuff. In older version it was possible to add...

Hey! A new tutorial for Apollo, somewhat similar to the existing one except: - uses a eukaryote genome (instead of bacteria), the same one as in the repeatmasker and funannotate...

Jbrowse2 tool

3

FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License permits unrestricted use (educational + commercial)...

TPUB:0000002 term is not found

8

## BUG/ERROR report At startup, I get this error: ``` INFO (PUB_IMPORT): Importing of publications is performed using a database transaction. If the load fails or is terminated prematurely then...