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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
Nicola Soranzo
@nsoranzo
@matthew-fogel You may want to check this Travis build failure: https://travis-ci.org/galaxyproject/tools-iuc/jobs/347170443
Jennifer Hillman-Jackson
@jennaj
@zfrenchee The tools Datamash and Group can be used to sum up data in tabular datasets. You'll need to first use the tool Concatenate to put all results into a single dataset. FeatureCount itself also can summarize counts by ReadGroup (see advanced options). If you didn't assign read groups during mapping, RG annotation can be added in with NGS: Picard > AddOrReplaceReadGroups. There are many ways to manipulate tabular data, but of these methods should produce the desired summary.
Martin Cech
@martenson
@bgruening is the circleci behaving well for you?
Björn Grüning
@bgruening
yes
just need to get the free OSX plan
thanks Martin
sorry that this is all so slow here, after the conference next week things will get better
Martin Cech
@martenson
Yeah it took you 4mins to respond and you have merely 22 o'clock, what is wrong with you???
^^ joke, good luck with the conference! Let me know if I can help.
Although I am sure it will be spectacular.
Björn Grüning
@bgruening
:) we will try
Matthew Fogel
@matthew-fogel
@nsoranzo I discovered my log file I use as expected output for the test still is containing the old version number. I'll submit a new pull request right now. But I wonder why the build passed for my PR #1743 (https://travis-ci.org/galaxyproject/tools-iuc/jobs/346341767) even though it failed after being merged to the master branch.
Nicola Soranzo
@nsoranzo
Strange indeed
Matthew Fogel
@matthew-fogel
@nsoranzo I see now when the Travis CI build for the PR ran my conda recipe with the newest version number had not been merged into conda yet (which is why it passed).
Nicola Soranzo
@nsoranzo
I was just checking that, good!
Matthew Fogel
@matthew-fogel
Thank you for all your help! I'll get on submitting the new PR now.
Alexander Lenail
@zfrenchee
@jennaj I'm having some file-format difficulties. I have a collection of tabular files (with format set to tabular) but these tools you've pointed me to tell me there's no tabular file collection in the history. Also @bgruening Multi-Join (combine multiple files) (Galaxy Version 1.1.1) (which I think is a tool of yours) says "No txt datasets in the history" but should probably work on tabular files as well, no?
Jennifer Hillman-Jackson
@jennaj
@zfrenchee Is this at Galaxy main https://usegalaxy.org or can you reproduce this there? A but report or share link to the history can be sent in and we can test to see what is actually going on (usage issue or some bug)
Send to galaxy-bugs@lists.galaxyproject.org (internal admin mailing list for usage, private not public). Or you can post the history share link here if having it public is not a factor
If you do send an email, please include a link to this convo
Alexander Lenail
@zfrenchee
@jennaj this was only happening for me when i copied some datasets from one history to another, so ignoring that...
I'm still finding it very difficult to sum counts from a couple counts files. Can you send me some more information about read groups?
I guess the larger question is: how are other folks building RNAseq workflows when samples are split across multiple lanes?
Alexander Lenail
@zfrenchee
Importantly, one component of this is the need to cherrypick datasets from collections:
Say I have a collection of 100 bams and I want to merge 4 of them into a new bam. Is there a way to select datasets from inside a collection, or at least, release a collection into a bunch of individual datasets in a history?
Alexander Lenail
@zfrenchee
Also, @bgruening is there a way to remove a reference genome / reference genome index from the galaxy database? I have an issue where the reference genome index can't be found by the aligner, but I also can't re-run the index-builder because there's already an entry in the database. Is there some way around this?
Björn Grüning
@bgruening
sure, you can remove the line from the loc file
Micropathology
@Micropathology
I'm having an issue installing iuc quast, I was asked to post this here https://biostar.usegalaxy.org/p/27018/#27038 , can anyone help?
Jennifer Hillman-Jackson
@jennaj
@zfrenchee Where are you working? Copied datasets should be usable or something is going wrong server-side.
Readgroups are in the BAM specification. You can also review Samtools docs about how to use them (I'm assuming you've already seen the galaxy tutorials by now :)
Alexander Lenail
@zfrenchee
@jennaj on one of my instances: answer.csbi.mit.edu. It looks like read groups isn't quite what I'm looking for -- it seems like a way to keep track of how to split bams rather than merge them.
Jennifer Hillman-Jackson
@jennaj
"Exploding a collection" or picking items from a collection to make a new collection are ideas/projects for future development. I'll let the dev team here comment more about that - and there are a few tickets around it that are open if you want to search in the galaxy repo
Readgroups can be used to merge data in an analysis, as well as split it out. It depends on the tool
But for what you want to do, simple text manipulation tools should work. I'd try to find out why the tabular dataset is problematic as a first step
Can you reproduce the data issue at one of the main public sites https://usegalaxy.org or https://galaxy.uni-freiburg.de? If not, then you'll know that something went wrong at your site by comparison
Jennifer Hillman-Jackson
@jennaj
The next Galaxy release is pending -- if there is a corner-case problem with tabular data, or using tab data in collections, it would be good to learn about it but we would need an example to troubleshoot usage/content versus a tool/server problem
Eg: might already be resolved in 18.01, might need to be fixed in 18.01....
Brad Langhorst
@bwlang
i'm having a bit of trouble with planemo... Traceback (most recent call last):
File "/home/NEB/langhorst/.planemo/gx_venv/bin/pip", line 7, in <module>
from pip import main
File "/home/NEB/langhorst/.planemo/gx_venv/local/lib/python2.7/site-packages/pip/init.py", line 13, in <module>
from pip.utils import get_installed_distributions, get_prog
File "/home/NEB/langhorst/.planemo/gx_venv/local/lib/python2.7/site-packages/pip/utils/init.py", line 26, in <module>
from pip._vendor import pkg_resources
File "/home/NEB/langhorst/.planemo/gx_venv/local/lib/python2.7/site-packages/pip/_vendor/pkg_resources/init.py", line 36, in <module>
import plistlib
File "/usr/lib/python2.7/plistlib.py", line 62, in <module>
import datetime
ImportError: No module named datetime
this is planemo 0.48 from conda = am i doing something dumb?
Brad Langhorst
@bwlang
deleting /home/NEB/langhorst/.planemo/gx_venv seems to have resolved the issue...
Jennifer Hillman-Jackson
@jennaj
How do others job config for Diffbind? Or any recommendations? We are seeing what look to be new memory fail errors with v 2.6.5.0 (newly installed on main)
@bgruening ^^ nate through you might know
Jennifer Hillman-Jackson
@jennaj
@bgruening another question - are mothur txt outputs whitelisted at Freiburg server? They do not display well at https://usegalaxy.org. galaxyproject/usegalaxy-playbook#70
Also having trouble extracting a workflow from my 16S test history - not sure why yet (updated tools causing problems? - a guess). I didn't test that at freiburg galaxyproject/usegalaxy-playbook#99
Björn Grüning
@bgruening
@jennaj we do have nothing special for diffbind, but we also just had a few hundrets of runs for this tool
Jennifer Hillman-Jackson
@jennaj
@bgruening thanks! maybe we should also leave it as is for now and see what happens for a while.
^^ @natefoo
Jennifer Hillman-Jackson
@jennaj
So - https://galaxy.uni-freiburg.de/ and https://usegalaxy.eu/ are not yet accessible. This might still be in progress (just found on the switch happened today). Question: will prior freiburg links be redirected to usegalaxy.eu? Thanks!
Björn Grüning
@bgruening
What do you mean with not accessible?
both links will stay
both websites will stay, just referencing to the same instance
Jennifer Hillman-Jackson
@jennaj
I get a 500 error. maybe need to clear my browser cache. let me check
Björn Grüning
@bgruening
both sites are up and running
Marius van den Beek
@mvdbeek
500 is internal server error, those are usually bugs or you're doing something very unexpected