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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Björn Grüning
@bgruening
please modify the galaxyp one
I think we are also fine to move this into tools-iuc if you think this is needed
Nicola Soranzo
@nsoranzo
galaxyp repo works for me, thanks!
Murilo Machado
@mrlmachado
Hi all, I found myself now, after some weeks trying to solve this, without any ideas for solving what I faced in my local galaxy server. I'm runing version 18.01 of galaxy with nginx and interactive environment enabled and postgresql and I build a tool with Gviz package dependency resolving by conda. Galaxy resolve all dependencies correctly but when I call IdeogramTrack function from R it throws a Bad Request 400 Error only within galaxy environment. If I execute from the server with Rscript, my code runs perfectly. I tried disable GIE and enable debug level of logs from nginx and wsgi but no success to find what is causing this error. I know this function call ucsc uri to download hg tables, but it works from the very server where galaxy is running and within galaxy it does not work. I really need help here to understand what is happening and how can I solve this out. Sorry for the long text and sorry again if this is not the right place to ask for help...
Nicola Soranzo
@nsoranzo
@mrlmachado You may have better luck on Join the chat: https://gitter.im/galaxyproject/Lobby
Brad Langhorst
@bwlang

just got this error when i tried to use a just installed copy of trim galore 

Failed to activate conda environment! Error was:
Not a conda environment: /mnt/galaxy/data/galaxy/tool-deps/_conda/envs/__trim-galore@0.4.3

Is this a tool bug or have I misconfigured my galaxy ? I recently upgraded, but conda resolution was working fine before .

Brad Langhorst
@bwlang
trimmomatic seems to have installed and worked… so maybe a tool issue?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
can you activate the environment ? this is not something that tools have control over
i.e source activate __trim-galore@0.4.3 with conda at /mnt/galaxy/data/galaxy/tool-deps/_conda/bin on PATH
Brad Langhorst
@bwlang
@mvdbeek - yep activates ok and trim-galore is on the path with correct version.
Brad Langhorst
@bwlang
to avoid methyldackel attempting (and failing sometimes) to create a fai index of the reference genome I’ve done this dirty hack to the wrapper
ln -s $reference_source.ref_file.fields.path reference.fasta &&
ln -s `dirname $reference_source.ref_file.fields.path`/../sam_indexes/**/*.fai reference.fasta.fai &&
Nicola Soranzo
@nsoranzo
@bwlang I think you can use $reference_source.ref_file.fields.files_path instead of `dirname $reference_source.ref_file.fields.path`
Lance Parsons
@lparsons
Is there a way to output a file from featureCounts that works both in DESeq2 as well as MultiQC? I'm a bit confused by the current options in version 1.6.0.2? @mvdbeek ?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Not sure, I haven't followed the discussions / updates. So the featurecounts output format has changed ?
Adapting this for multiqc while breaking deseq2 sounds like a bad deal
(if that's what happened)
Brad Langhorst
@bwlang
@nsoranzo that solves one ugliness, but i’m not sure about searching a subtree for an fai… is that likely to work reliably on other galaxys. Maybe i should just change the tool to use ths sam_indexes ref source...
Lance Parsons
@lparsons
Yeah, looking a bit deeper, it seems it was this line: https://github.com/galaxyproject/tools-iuc/pull/1664/files#diff-9c6098d25fe7aa5d7d90c3e2c9ff4aebR178
@mblue9 Have you tested this? Am I right in assuming DESeq2 doesn't work with the "MultiQC Compatible" output from FeatureCounts?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
OK, you have to select tabdel_short now
but the bigger issue is these mega PRs are barely reviewable
because that change should really not have passed as everyone has to update their workflows now
Lance Parsons
@lparsons
Agreed. And worse, I can't realistically use featurecounts, deseq2, and multiqc in the same workflow?! That's not right. MultiQC and DESeq2 should take the same input. Those should be fixed, not have featurecounts effectively broken...
Hrm.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Also this is pretty suboptimal because now you've got to run featurecounts once for multiqc and once for deseq2 or drop the header before passing into deseq2.
Lance Parsons
@lparsons
Agree completely.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
On top of that featurecounts doesn't start the head with #, so we can't just handle that in deseq2
Lance Parsons
@lparsons
Not sure how to fix this exactly, but it seems there should be a reasonable way to handle it. Perhaps adding the header in the MultiQC wrapper from the metadata?
That is pretty nasty trickery (and not really documented, afaik), but it seems it would keep the other tool wrappers (deseq2 and featurecounts) clean.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
yeah, I think that'd be better
Lance Parsons
@lparsons
Is there an example of this anywhere you know of? Grabbing the metadata I mean (and perhaps adding it as a header line). I seem to remember seeing something like this before. Might be nice to have this as a built in option that tool authors could specify (some verion of the input file with headers as the first line..., but that's a bit too long term for this.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
I suppose you can construct this from the element identifier
Lance Parsons
@lparsons
No, I don't think so, since it there could be mulitple columns, right? At least in theory.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Well that format doesn't work for deseq2 at all
Lance Parsons
@lparsons
Also, I'm curious why this works with edgr and limma-voom
That's not really great either...
Ghost
@ghost~5772e7e2c2f0db084a206e1b
It's another approach ...
Lance Parsons
@lparsons
But a bit of a bigger problem to solve...
MultiQC needs to be able to take as wide a range of outputs from FeatureCounts as possible, imho.
If DESeq2 is constrained, so be it.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
So for the deseq2-style output you could write a configfile that just contains Geneid $input1.element_identifier and then < $configfile $input1 > multiqc_input.tab or sth. like that
The other DE wrappers take the header format, so that wouldn't be an issue
Lance Parsons
@lparsons
Or should we just allow DESeq2 to accept the header format? And output the header line with a leading #?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
That'd be OK as well, I think
Sounds less complicated, if i think about it :D
Well, we can treat a line that starts with Geneid as a header line in deseq2, I think that'd be better than manipulating the featurecounts output
who knows who's depending on that ...
(if I ever discover a gene I'll name it Geneid though :D)
Lance Parsons
@lparsons
I'd be OK with that and then removing the DESeq2 specific output from FeatureCounts...
Ghost
@ghost~5772e7e2c2f0db084a206e1b
:+1: