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galaxybot
@galaxybot
[natefoo] The first 'g2main' is the Galaxy username, second 'g2main' is the group. /galaxy-repl/main/ftp/%U is the homedir path.
[gronke] wat
[gronke] sorry I dont know what that is, is that an sql query?
[gronke] oh wait that's the query from the conf file, sorry
[natefoo] Yes. Do you not have a SQLNamedQuery? You must if you've successfully authenticated your Galaxy users in ProFTPD
[gronke] let me compare that ot mine
[natefoo] Ok
[gronke] SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN substring(password from 1 for 6) = 'PBKDF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,512,512,'/galaxy_share/database/files/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"
[gronke] so I dont have the g2main stuff
[natefoo] What's uid 512? `getent passwd 512`
[natefoo] Ah that's the uid in the example.
[gronke] oops
[gronke] so I need to set that to galaxy's uid/gid
[natefoo] Yeah, or just its user name and group name,
[gronke] let's see if this works
[gronke] hmm, now I can't log in at all. Control Transfer Error.
galaxybot
@galaxybot
[gronke] From the proftpd logging: ERROR: column "galaxy" does not exist
[gronke] that's no good
[natefoo] Make sure you quote strings
[natefoo] 512 is unqouted but you'd need 'galaxy' if using the name
[gronke] it worked when I used the uid/gid numbers
[gronke] thanks man
[natefoo] cool
[gronke] just logged in and the newly created user folder is owned by galaxy
Jennifer Hillman-Jackson
@jennaj
Community question "Is there any way to run a workflow with step Parameters through blend4J?" Does anyone know? Full post: https://help.galaxyproject.org/t/galaxy-api-run-workflow-with-parameters/1406
galaxybot
@galaxybot

[unknown]
HISAT2 error: Auto-detection [usegalaxy.org support] error
Hey,

I have an error from HISAT2. Some of the samples are errors and others have this:

[Capture3]

Auto-detect is actually heplful. HISAT2…

galaxybot
@galaxybot

[unknown]
Use samtools to Count the read which Counter tools cant Count. [usegalaxy.org support] tool-dev
Hi

if there is a low MAPQ in my reads . someone tells me to Use samtools view in.bam "chr1:234-567" to explore the reads in the region of…

Pablo Moreno
@pcm32
Hi, anyone doing development on pycharm with Galaxy? How would you setup the run from pycharm so that the python process is controlled by pycharm and you can use things like the debugger? It used to be easy to call paster.py, but with the newer setup it is not clear to me.... thanks!
hamodi86h
@hamodi86h
Hi
I tried hardly to analyse RPKM data using EdgeR and DESeq2 but I couldn't? do you please have sample of the Txt files or if you can guide me to a useful link. Thanks
Marius van den Beek
@mvdbeek
@pcm32 that still works
Screen Shot 2019-05-29 at 12.29.50.png
Pablo Moreno
@pcm32
brilliant, thanks @mvdbeek !
still with config.ini?
Marius van den Beek
@mvdbeek
yeah, can't be bothered to update :D
Brad Langhorst
@bwlang
it seems that after upgrade some users cannot import data from the library_import_dir
these users have a symlink with their email address pointing to a common shared folder (“production”). The import directories contain symlinks to the actual fastq data location - users can see the only file that is not a symlink (a text file). any recent changes to the user_library_import_symlink_whitelist features?
(i’m looking at the commit list, but thought somebody might just know…)
galaxybot
@galaxybot

[unknown]
How to extract unique reads from SAM file [usegalaxy.org support]
Hi.

How can I extract uniquely and concordantly paired-end mapped reads (aligned concordantly exactly 1 time) from HISAT2?

Thanks

Brad Langhorst
@bwlang
if i move the symlinks to hard links import works fine.
galaxybot
@galaxybot
[unknown]
account has been marked deleted, [usegalaxy.org support]
My accounts were active last night and running data, however this morning I tried logging in to find a message saying the account had been m…
Martin Cech
@martenson
@bwlang nothing comes to mind, could you create an issue please?
Marius van den Beek
@mvdbeek
that's an update from 19.01 or 18.09 ? I think there were some changes from 18.09 to 19.01
Brad Langhorst
@bwlang
i think i came from 18.09...
i’ll have a look at those commits
Will Simpson
@simpsonw
Is the @local_extra_dirs decorator in lib/galaxy/objectstore/__init__.py considered deprecated? It's referenced all over the place in lib/galaxy/objectstore/rods.py but that hasn't been under active development for a long time and the only other reference I see to it is in a comment. The Git log only mentions it a couple times back in 2013. Perhaps it should be removed?
Qiang Gu
@qiagu
Hi everyone, Is there a simple way to rerun multiple failed jobs? I have ~70 jobs failed from a collection. Rerunning them one by one would give me headache.
galaxybot
@galaxybot

[unknown]
Half of data is missing (black) in plotheatmap heatmap [Uncategorized]
When creating a heatmap in plotheatmap, only genes from the -2kb to TSS are displayed, everything from TSS to 2kb is black:

I used computem…

galaxybot
@galaxybot

[unknown]
Problem with intersect tool [usegalaxy.org support]
Hi all, I have a problem in intersecting two datasets (one in bed and the other in bedgraph format).

Here is the error message:

Traceback …

galaxybot
@galaxybot
[unknown]
mapping RNA-seq data to a composite build of bacterial genomes [usegalaxy.eu support]
Hi, Hope you can help: I’m trying to map some RNA-seq data generated from libraries prepared from RNA extracted from swabs taken from mouse …