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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
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    Maux82 commented #338
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  • Jan 30 2019 18:12
    bgruening commented #338
  • Jan 30 2019 10:24

    bgruening on tmgowan-flashlfq

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  • Jan 30 2019 10:24
    bgruening commented #339
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    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
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  • 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
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  • Jan 23 2019 06:38

    bgruening on unipept4.0

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  • 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)

Yasset Perez-Riverol
@ypriverol
I need to ask in the issue
I already ask
Carlos
@CarlosHorro
@ypriverol @bernt-matthias When I was testing MetaMorpheus, it didn’t work with the last Mono version available at that time (about Dec. 2020), but it did work using dotnet conda package in my local. However, as @bgruening said, there was an issue with the libc version required by that dotnet conda package, higher than the ones supported by bioconda
@bgruening I can test MetaMorpheus again with that Mono version
Yasset Perez-Riverol
@ypriverol
That would be amzizyng @CarlosHorro
Carlos
@CarlosHorro
Hi all, I’m afraid MetaMorpheus still doesn’t work with Mono
I’ve tried it with both Mono 5.14.0.177 Conda package and the one installed on my local machine (more modern), and they don’t work
M Bernt
@bernt-matthias
Would it help if we include metamoepheus in conda-forge?
Björn Grüning
@bgruening
conda-forge is also building with the older centos afaik
M Bernt
@bernt-matthias
My suggestion was just based on the intuition that if they build .net then it should also be usable within the same framework.
not compiling, just dowloading precompiled packages :(
M Bernt
@bernt-matthias
Hmm. So they have this requirement on glibc (https://github.com/conda-forge/dotnet-feedstock/blob/85a20eb2b9fe17d804de5e0208e583eb5ddd5005/recipe/meta.yaml#L56) which leads to the error in bioconda (I guess). So I would expect that the conda-forge build system can cope with this requirement.
Björn Grüning
@bgruening
but this will still not make it executable on older HPC systems
M Bernt
@bernt-matthias
OK. Do you know if conda will then not allow to install such a package .. if the system is to old? How about (mulled) containers?
Björn Grüning
@bgruening
containers can work imho
conda will most likely not work
on such systems
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.
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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.
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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.
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Fri Apr 09 18:11:24 CEST 2021 Checking spectra for T4A_1.msgf.mzid.gz.
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Fri Apr 09 18:11:24 CEST 2021 Importing PSMs from T4A_1.msgf.mzid.gz
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Fri Apr 09 18:11:33 CEST 2021 Parsing T4A_1.omx.gz.
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Fri Apr 09 18:11:55 CEST 2021 Checking spectra for T4A_1.omx.gz.
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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