Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • 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
Lucille Delisle
@lldelisle
Thx @bernt-matthias
Dan Fornika
@dfornika
Sorry to ask again, but could someone please review this PR that adds support to tetyper for loading variant profiles from tool data tables? Thanks! galaxyproject/tools-iuc#2772
Björn Grüning
@bgruening
on it @dfornika !
Greg Von Kuster
@gregvonkuster

I'm working with a lab doing research with bacterial genomes and I'm working on introducing their pipeline into Galaxy. In many cases the bacterial data consists of a combination of species, so mapping to a specific genome is tricky.

Mapping bacterial data to a referencce genome has 3 options:

  1. the genome is known, so is selected from local cache as is often done in Galaxy

  2. a custom reference is selected - these custom references are a composition of files, and I'm not aware if/how this is currently handled in Galaxy. For example, for the custom reference for Brucella_abortus1 consists of the following 7 files:

    • Bab1_define_filter.xlsx
    • Bab1_remove_from_analysis.xlsx
    • NC_006932-NC_006933.fasta
    • NC_006932-NC_006933.gbk
    • NC_006932-NC_006933.genome
    • NC_006932-NC_006933.gff
  3. The input data is inspected to determine the optimal genome to be mapped.

Does anyone know if this is currently being done in Galaxy? I've done some searching and only found this so far https://help.galaxyproject.org/t/mapping-rna-seq-data-to-a-composite-build-of-bacterial-genomes/1443.

I can wrap the tool for Galaxy that the lab is using, but I want to make sure I'm not re-inventing the wheel.

Jennifer Hillman-Jackson
@jennaj
Could someone who knows more about the status of GATK4 wrapper dev reply to this post? I see a few in done, some in progress, but didn't find a master ticket summary -- maybe missed it? Thx! https://help.galaxyproject.org/t/galaxy-tool-wrappers-for-gatk-4/2798
M Bernt
@bernt-matthias
Do you think its good practice to list the allowed data types in a data input in the label or the help?
e.g. select tsv data sets(s)
Nicola Soranzo
@nsoranzo
:+1:
M Bernt
@bernt-matthias
Maybe the Galaxy web UI should just do this? similar to -argument.
Nicola Soranzo
@nsoranzo
That's a very good idea!
M Bernt
@bernt-matthias
Anton Nekrutenko
@nekrut
Someone removed interleaved fastq input option from bwa (0.7.17) This is not good. Previous version (0.7.15) does have it
.... wait ... I think I'm crazy = its there, sorry
Björn Grüning
@bgruening
We all now that you love the interleaved format and would never remove this option ;)
M Bernt
@bernt-matthias
fancy tool dev question regarding the command cheetah code: how could one get a dictionary containing the parameter names as keys and the parameter values as values?
M Bernt
@bernt-matthias
fancy :) might work .. I guess the json file contains the structure implied by sections and conditionals?
Wolfgang Maier
@wm75
I guess so, but I've never tried it myself
Slugger70
@Slugger70
Is there any reason that linting is taking so long on Travis? PR#2795 (Build #10920) linting has been running for over 20 minutes. Even though the output say that the build exited with 0.
Björn Grüning
@bgruening
mh, testing is finished already
Nicola Soranzo
@nsoranzo
I think it's a refresh issue on Travis, the build is green now.
I've seen the same today on another unrelated project using TravisCI.
Björn Grüning
@bgruening
@Slugger70 you should remove the parameter completey I guess if they do not exist anymore
Slugger70
@Slugger70
k
Thanks
Greg Von Kuster
@gregvonkuster
Does anyone know a quick proper fix for this galaxyproject/tools-iuc#2783 Could this be caused by a recent change in the data manager framework?
M Bernt
@bernt-matthias
Maybe you can test this galaxyproject/galaxy#9243
John Chilton
@jmchilton
Does anyone have an examples of "real world" workflow reports?
Wolfgang Maier
@wm75
Already generated with Galaxy or with something else?
John Chilton
@jmchilton
With Galaxy
I want to generate or find some more real world screenshots
Nolan Woods
@innovate-invent
Hey guys, I need a category added to the main tool shed for generic math algorithms. A tool that calculates sha256 and a tool that does clustering of distance matrices are what I have in mind
Dan Fornika
@dfornika
Could I request that this be merged? galaxyproject/tools-iuc#2831
Slugger70
@Slugger70
Done
Dan Fornika
@dfornika
Could this be merged too? It updates iqtree to handle custom models correctly: galaxyproject/tools-iuc#2835
Wolfgang Maier
@wm75
Done, too
Dan Fornika
@dfornika
Thanks!
Björn Grüning
@bgruening
:heart:
JayanthiGangiredla
@JayanthiGangiredla
Hi, Can you please update data managers for busco. Looks like Busco team has moved their databases to new location from the one before. The new location URL is http://busco-archive.ezlab.org/datasets/ for all the databases. Please help!
Marius van den Beek
@mvdbeek
Screenshot 2020-01-30 at 12.39.23.png
starting to look really good
M Bernt
@bernt-matthias
hooray. what is left?
Marius van den Beek
@mvdbeek
let me upload the failed stuff
Nicola Soranzo
@nsoranzo
qiime and maker?
Marius van den Beek
@mvdbeek
I’ve excluded both, qiime is unable to create proper biom files
I have no idea what’s going on there
make takes forever to test
and fills up my hard disk locally
there is a chance we can get qiime to work though, since it passed travis tests prior to containerizing