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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
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    nsoranzo commented #2267
Björn Grüning
@bgruening
@lecorguille planemo-dev should have this
Jennifer Hillman-Jackson
@jennaj
@lparsons Hi - there is a question about the install of Cutadapt in a local. Could you help them? https://biostar.usegalaxy.org/p/27434/
Jennifer Hillman-Jackson
@jennaj
@jj-umn @bwlang GMAP/MiGMAP question https://biostar.usegalaxy.org/p/27374/
I am not sure which tool version, Galaxy version, etc is in use and I pointed them here for help. I don't know either of these wrappers well enough to help.
Alexander Lenail
@zfrenchee
What is the system path for the local reference data config file in galaxy?
Jennifer Hillman-Jackson
@jennaj
A thank you for the featureCounts annotation update! Nice! https://biostar.usegalaxy.org/p/27461/
Björn Grüning
@bgruening
@jennaj such a big difference is scary isn't it?
Jennifer Hillman-Jackson
@jennaj
yeah, it's the gene_id/transcript_id being the same value in UCSC GTFs. I know why the TB outputs the data that way but many people completely miss it .. and then get odd results --since the counts are really by transcript, not gene :(
Björn Grüning
@bgruening
either way I added a small comment to biostar, feel free to accept the answer :)
Jennifer Hillman-Jackson
@jennaj
:)
Jennifer Hillman-Jackson
@jennaj
Hi - does anyone know if there are plans to wrap the Torrent Suite? https://github.com/iontorrent/TS
From a question at Biostars: https://biostar.usegalaxy.org/p/27473
Björn Grüning
@bgruening
Not that I'm aware of.
Jen IonTorrent was a sponsor for GCC at some point right?
Mabye they are interested in developing integrations?
If they have someone to work on it, I'm happy to help.
look at that?
would be nice to ping them, if they are willing to update them and maybe contribute to IUC or offer conda integration
Jennifer Hillman-Jackson
@jennaj
ooh - I couldn't find that link!
Ok, I'll share that with the biostar post. I think someone from IUC should make contact, yes? And they were a sponsor, maybe this will work out :)
Björn Grüning
@bgruening
@jennaj I think you should make contact :)
You Main team member :)
Jennifer Hillman-Jackson
@jennaj
Ah, ok, will check with team first to make sure there isn't some contact going on already. Thanks!
Björn Grüning
@bgruening
Thanks Jen!
mblue9
@mblue9
Thanks to @jennaj and @bgruening for the notifications about those Biostars posts on Cutadapt featureCounts! (It made me finally get around to making a Biostars account :smile:)
Jennifer Hillman-Jackson
@jennaj
@CollardT You are working on the updated Ballgown wrapper, correct? A question came in about an error.
I haven't seen this before so don't know how to solve it or if this is a known issue -- is there anything you would like to add to my reply? https://biostar.usegalaxy.org/p/27454/
The tool is not installed at either usegalaxy.* .. so this error is on a local, docker, etc with the tool installed from the existing MTS repo
Jennifer Hillman-Jackson
@jennaj
Is this a bug with Salmon output files? Or should the output format be configurable?
Seems like a normal use case, but I haven't used the tool that much. https://biostar.usegalaxy.org/p/23985/#27525
Oleksandr Moskalenko
@moskalenko
I'm doing a lot of tool installs to switch to conda for 18.01 from my much older previous production instance and I'm noticing a few broken packages in the toolshed. Where should I report the bugs?
Nicola Soranzo
@nsoranzo
Depends on who's the tool author/owner
Oleksandr Moskalenko
@moskalenko
What about devteam and iuc
Oleksandr Moskalenko
@moskalenko
Got it, thanks Bjorn.
Jennifer Hillman-Jackson
@jennaj
@yhoogstrate Do you know if there are plans to update Varscan to include the newer "somatic" function? If not, what would be your (and others) suggested tool alternative?
question was asked here: https://biostar.usegalaxy.org/p/27507/
Oh! I found the tools at usegalaxy.eu. Not sure how I missed those in the MTS! I'll point the user to the other server. Tx!
Alexander Lenail
@zfrenchee
Is it possible in 18.01 to run tools on subsets of collections, or to "explode"/"eject" collections into individual history items?
Alexander Lenail
@zfrenchee
@jmchilton
John Chilton
@jmchilton
You can drag and drop individual items into the tool form - if you have a more systematic way to indentify the elements there is also a tool that filters a collection from a tabular file - this isn’t super straight forward but it enables a high level of tracking and use within workflows
There isn’t an explode tool though in 18.05
I meant 18.01
Alexander Lenail
@zfrenchee
Thanks!
Jennifer Hillman-Jackson
@jennaj
Does anyone know if Deseq2 in Galaxy can be configured to run with single-end data? Or is paired-end input required?
Björn Grüning
@bgruening
paired end is not required
DeSeq2 is only taking counts and don't care about single/paired
Jennifer Hillman-Jackson
@jennaj
Ok, there must be something else wrong with the inputs. Another bug report had the same error message and paired end inputs were used. There was only one replicate per condition in that example - maybe the counts are too sparse to do the DE.
Dave B.
@davebx
whomever implemented the sort flag for tool test outputs, I owe you a beer