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  • Jan 31 2019 22:04
    foellmelanie closed #336
  • Jan 31 2019 22:04
    foellmelanie opened #340
  • Jan 31 2019 13:58
    Maux82 commented #338
  • Jan 31 2019 13:36
    Maux82 commented #338
  • Jan 30 2019 19:39
    Maux82 synchronize #338
  • Jan 30 2019 18:12
    bgruening commented #338
  • Jan 30 2019 10:24

    bgruening on tmgowan-flashlfq

    (compare)

  • Jan 30 2019 10:24
    bgruening commented #339
  • Jan 30 2019 10:24
    bgruening closed #339
  • Jan 30 2019 10:24

    bgruening on master

    Modify for new FlashLFQ release… new test data for new version Merge pull request #339 from ga… (compare)

  • Jan 28 2019 20:49
    tmcgowan review_requested #339
  • Jan 28 2019 20:49
    tmcgowan opened #339
  • Jan 28 2019 20:45

    tmcgowan on tmgowan-flashlfq

    Modify for new FlashLFQ release… new test data for new version (compare)

  • Jan 28 2019 14:56
    bgruening commented #338
  • Jan 28 2019 14:54
    bgruening synchronize #338
  • Jan 28 2019 14:10
    Maux82 synchronize #338
  • Jan 27 2019 14:11
    bgruening synchronize #338
  • Jan 27 2019 14:02
    Maux82 opened #338
  • Jan 23 2019 06:38

    bgruening on unipept4.0

    (compare)

  • Jan 23 2019 01:47

    jj-umn on master

    unipept version 4.0 Currently … unipept.py - best_match of tryp… Remove extraneous text and 2 more (compare)

Björn Grüning
@bgruening
everywhere else yes
M Bernt
@bernt-matthias
Thanks for the explanations. Then mono would still be the best option. @CarlosHorro how bad does it look if you compile with mono, maybe the metamorpheus developers can fix it?
Björn Grüning
@bgruening
@bernt-matthias if its just for Galaxy, we can simply create a Docker container and use that
we do this for msconvert as well
Carlos
@CarlosHorro
Um… I will open an issue in Metamorpheus GitHub in order to get an idea about how the probabilities of running over Mono looks like...
Carlos
@CarlosHorro
Hi @bgruening @bernt-matthias , in a past meeting with galaxy-p people we had PS crashing some times in usegalaxy.eu, but I was not able to see the internal problem as I didn’t have access to the error output and the standard output didn’t show the details. Now we were adding an option to SG & PS in order to avoid writing to the log but instead writing everything to the standard output , so we can see internal errors when we don’t have access to the error output.
However, I still see that errors are being shown in the error output in the same way than it did… is there something I’m missing?
Björn Grüning
@bgruening
Not sure, but if you have a job ID please ask me and I can give you all logs
M Bernt
@bernt-matthias
Really good idea.
Carlos
@CarlosHorro
Thank you, I see this:
Job API ID: 11ac94870d0bb33a32644780630b1288
Björn Grüning
@bgruening
An error occurred when saving the path preference to /usr/local/tools/_conda/envs/mulled-v1-908940fc14782dcdd3b450ac0494c189161b102814738a5a8bf51db12b8266ea/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt.
Fri Apr 09 18:09:36 CEST 2021 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Fri Apr 09 18:10:44 CEST 2021 Import process for Galaxy_Experiment_2021040918091617984562

Fri Apr 09 18:10:45 CEST 2021 Importing sequences from input_fasta_file.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Fri Apr 09 18:11:13 CEST 2021 Establishing local database connection.
Fri Apr 09 18:11:13 CEST 2021 Reading identification files.
Fri Apr 09 18:11:13 CEST 2021 Parsing T4A_1.msgf.mzid.gz.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Fri Apr 09 18:11:24 CEST 2021 Checking spectra for T4A_1.msgf.mzid.gz.
10% 20% 30% 40% 50% 60% 70% 80% 90%
Fri Apr 09 18:11:24 CEST 2021 Importing PSMs from T4A_1.msgf.mzid.gz
 50% 60% 70% 80% 90% 100% 110% 120% 130% 140%
Fri Apr 09 18:11:33 CEST 2021 Parsing T4A_1.omx.gz.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Fri Apr 09 18:11:55 CEST 2021 Checking spectra for T4A_1.omx.gz.
10% 20% 30% 40% 50% 60% 70% 80% 90%
Fri Apr 09 18:11:55 CEST 2021 Importing PSMs from T4A_1.omx.gz
Fri Apr 09 18:11:56 CEST 2021 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /data/dnb03/galaxy_db/job_working_directory/016/538/16538684/working/resources/PeptideShaker.log</CompomicsError>
PS tries to write into the conda env :(
Carlos
@CarlosHorro
yep that is the standard output, but the error one?
Björn Grüning
@bgruening
where should that be
in the working directory?
galaxy@sn06:/data/dnb03/galaxy_db/job_working_directory/016/538/16538684$ ll working/
total 182
-rw-r--r--. 1 galaxy galaxy     0 Apr  9 18:09 conda_activate.log
drwxr-xr-x. 2 galaxy galaxy     0 Apr  9 18:09 output_reports
drwxr-xr-x. 8 galaxy galaxy   333 Apr  9 18:10 PeptideShakerCLI
drwxr-xr-x. 2 galaxy galaxy    68 Apr  9 18:10 resources
-rw-r--r--. 1 galaxy galaxy 25652 Apr  9 18:09 SEARCHGUI_IdentificationParameters.par
lrwxrwxrwx. 1 galaxy galaxy    82 Apr  9 18:09 searchgui_input.zip -> /data/dnb03/galaxy_db/files/4/6/6/dataset_4664e332-7d1c-4438-b854-53dac5af6dd4.dat
galaxy@sn06:/data/dnb03/galaxy_db/job_working_directory/016/538/16538684$ ll working/PeptideShakerCLI/
total 153093
-rw-r--r--. 1 galaxy galaxy       23 Apr  9 18:09 exportFactory.json
drwxr-xr-x. 2 galaxy galaxy       29 Apr  9 18:10 fastaSummary
drwxr-xr-x. 2 galaxy galaxy      268 Apr  9 18:09 gene_mapping
drwxr-xr-x. 2 galaxy galaxy        0 Apr  9 18:09 identification_parameters_4
drwxr-xr-x. 2 galaxy galaxy        0 Apr  9 18:11 matches
drwxr-xr-x. 2 galaxy galaxy        0 Apr  9 18:09 pride
-rw-r--r--. 1 galaxy galaxy 46133273 Apr  9 18:10 T4A_1.cms
-rw-r--r--. 1 galaxy galaxy 83500281 Apr  9 18:10 T4A_2.cms
-rw-r--r--. 1 galaxy galaxy     1466 Apr  9 18:09 utilities_userPreferences.cup
Carlos
@CarlosHorro
yep that log file, /data/dnb03/galaxy_db/job_working_directory/016/538/16538684/working/resources/PeptideShaker.log<
Björn Grüning
@bgruening

Fri Apr 09 18:09:33 CEST 2021: PeptideShaker version 2.0.15.
Memory given to the Java virtual machine: 4151836672.
Total amount of memory in the Java virtual machine: 2075918336.
Free memory: 2041558912.
Java version: 11.0.8-internal.
java.lang.RuntimeException: java.io.FileNotFoundException: /usr/local/tools/_conda/envs/mulled-v1-908940fc14782dcdd3b450ac0494c189161b102814738a5a8bf51db12b8266ea/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Read-only file system)
        at com.compomics.util.io.flat.SimpleFileWriter.<init>(SimpleFileWriter.java:59)
        at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.writeConfigurationToFile(PeptideShakerPathParameters.java:391)
        at eu.isas.peptideshaker.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:110)
        at eu.isas.peptideshaker.cmd.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:269)
        at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1366)
Caused by: java.io.FileNotFoundException: /usr/local/tools/_conda/envs/mulled-v1-908940fc14782dcdd3b450ac0494c189161b102814738a5a8bf51db12b8266ea/share/peptide-shaker-2.0.15-0/resources/conf/paths.txt (Read-only file system)
        at java.base/java.io.FileOutputStream.open0(Native Method)
        at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:237)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:187)
        at java.base/java.io.FileWriter.<init>(FileWriter.java:96)
        at com.compomics.util.io.flat.SimpleFileWriter.<init>(SimpleFileWriter.java:53)
        ... 4 more
java.io.FileNotFoundException: /data/dnb03/galaxy_db/job_working_directory/016/538/16538684/working/PeptideShakerCLI/exportFactory.json (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at com.compomics.util.io.json.JsonMarshaller.getJsonStringFromFile(JsonMarshaller.java:227)
        at com.compomics.util.io.json.JsonMarshaller.fromJson(JsonMarshaller.java:142)
        at eu.isas.peptideshaker.export.PSExportFactory.loadFromFile(PSExportFactory.java:158)
        at eu.isas.peptideshaker.export.PSExportFactory.getInstance(PSExportFactory.java:99)
        at eu.isas.peptideshaker.cmd.ReportCLIParams.<clinit>(ReportCLIParams.java:17)
        at eu.isas.peptideshaker.cmd.PeptideShakerCLIParams.createOptionsCLI(PeptideShakerCLIParams.java:76)
        at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1370)
Carlos
@CarlosHorro
in the job information area, there are usually 2 row, one with Tool Standard Output:, and another one with "Tool Standard Error:”. This one is not available in usegalaxy.eu :-(
um great, thank you very much
it is weird because I don’t see any error specific of this job
other jobs were sucessfully executed into the same server
Björn Grüning
@bgruening
yes, there is some bug, that sometime, not always the stderr is not transferred back
we still work on understanding this
M Bernt
@bernt-matthias
I think there are already issues for those errors
Carlos
@CarlosHorro

I think there are already issues for those errors

yes, there are

M Bernt
@bernt-matthias

The IWC (Intergalactic Workflow Commission) has recently made some progress:

  • we have now automated testing of submitted workflows (with planemo)
  • and we also have automatic deployment (which allows easier installation on Galaxy instances)

IWC would be happy about submissions of workflows. So if you have finished workflows open a PR over here: https://github.com/galaxyproject/iwc

Carlos
@CarlosHorro
Hi @bernt-matthias , I wanted to ask you about the strategy followed by MetaMorpheus developers in order to make it to work in conda-forge Conda package. It internally seems to use dotnet, but checking the installed software in Ubuntu it has the appearence of a Linux package. Do you think that, with that structure, would it be possible to apply there the same approach you suggested me for xtandem (ie: replacing PS provided MetaMorpheus binaries by the ones included in the MetaMorpheus conda package)? Thank you...
M Bernt
@bernt-matthias
Jep. It just works on Linux. I think it would be great to install mm via conda and ignore/remove the one provided by PS/SG (as we already do for xtandem). For mm we need to check if there is a difference how to call it. I think we should do this for as many of the 3rd party tools as possible. Maybe step by step.
Carlos
@CarlosHorro
Thank you. Yes, it is called differently, so I will have to include some internal checks to PS in order to detect if it is running in a Conda environment or as usual
Carlos
@CarlosHorro
Hi all, we have done some tests with MetaMorpheus working on SG Galaxy tool :-) When next app version is ready I will work on it in bioconda and galaxy :-)
Björn Grüning
@bgruening
:heart:
M Bernt
@bernt-matthias
+1
M Bernt
@bernt-matthias

Anyone using this tool successfully for downloading large data sets https://github.com/galaxyproteomics/tools-galaxyp/blob/master/tools/uniprotxml_downloader/uniprotxml_downloader.xml .. large means millions of fasta sequences.

We always get Connection reset by peer

Melanie C. Föll
@foellmelanie
we have never used this tool at all, we only use Protein Database Downloader
M Bernt
@bernt-matthias
@foellmelanie an this Download all proteins given a list of taxids?
Melanie C. Föll
@foellmelanie
nah, sorry it seems not to work with taxids, you need to manually select out of the given options
M Bernt
@bernt-matthias
I just started to update the uniprot downloader (galaxyproteomics/tools-galaxyp#601) .. Wondering if there is interest in more complex queries in the community. Currently we use only the taxonomy field .. but there are so many more: https://www.uniprot.org/help/query-fields
Melanie C. Föll
@foellmelanie
we cannot help here, we work mainly with human, few times with mouse...
Johan Gustafsson
@supernord
Hi all: question about MaxQuant - what is the largest (by number of samples) MaxQuant run that has been completed on GalaxyEU?
Melanie C. Föll
@foellmelanie
we were running about 100 relatively empty/small co-ip files
Johan Gustafsson
@supernord
Thanks @foellmelanie: do you know if anyone has tried similar numbers of samples but with full size LC-MS/MS raw files (700-800 MB range each)?
Björn Grüning
@bgruening
@supernord do you see any problems with that? More resources needed?
Melanie C. Föll
@foellmelanie
@supernord https://galaxyproject.eu/posts/2020/04/14/integrative-meta-omics/ 144 raw files, each 1GB run on EU Server
aheikema
@aheikema
Dear all, I am new at proteomics data analysis. Im looking for a galaxy tool that can do an orthology analysis on a maxquant dataset of bacterial samples. Can someone advice me what to use, preferably with an tutorial?
aheikema
@aheikema
I’m not a bioinformatician but okay to use Galaxy. Many thanks.
aheikema
@aheikema
Thanks, but tool seems to need fasta files. I have a txt file with protein IDs.
M Bernt
@bernt-matthias
@aheikema then you may subset the fasta file that has been used in MaxQuant with the ids.
M Bernt
@bernt-matthias
Any objections to updating CI/CD galaxyproteomics/tools-galaxyp#654 .. brings it in sync with the IUC repo
Björn Grüning
@bgruening
no :)