Hi, I am getting /usr/bin/docker-current: Error response from daemon: driver failed programming external connectivity on endpoint adoring_engelbart (33ba8ed4cceaa86424363b5a9f1635ebf4ebb641c47c24c714f2ee1fe8846663): Bind for 0.0.0.0:10401 failed: port is already allocated.
opening the http://localhost:10401/ shows the default Apache2 Ubuntu Page docker ps CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 799753202ce1 ebf55696681a "apache2ctl -DFORE..." 11 hours ago Up 11 hours 0.0.0.0:10401->10401/tcp dazzling_mahavira Am Donnerstag, 29. November 2018 01:32:55 UTC+1 schrieb Eric Deutsch: > > Hi Robert, thanks for testing. Based on our testing, we now changed the > calling sequence for starting Petunia to this: > > > > *docker run -dit --user=root -p 10401:10401 -v /tmp/tppdata:/data > spctools/tpp apache2ctl -DFOREGROUND* > > > > as described in the refreshed tutorial: > > > http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image > > > > Let us know what you think of that! > > > > Regarding your precautions question, it seems to depend on how Docker is > installed on your system. If you have to run `sudo docker` for each > command, then things are written as root. On one of our computers, the IT > guys have jailed the user docker runs as as UID 100000, so that’s a little > different. So I’m not sure the best advice here. In the tutorial we suggest > do a `chmod 777` that seems to make things work out nicely. On Windows, it > should all be find if the user has admin privileges. But there still might > be problems if the user doesn’t have admin privileges? I’m uncertain. I > haven’t tested that yet. > > > > Regards, > > Eric > > > > > > > > *From:* [email protected] <javascript:> < > [email protected] <javascript:>> *On Behalf Of *Robert > *Sent:* Tuesday, November 27, 2018 3:17 AM > *To:* spctools-discuss <[email protected] <javascript:>> > *Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker > > > > > Sure, Eric! Could you please give me the recommended command line > parameters for running TPP Petunia on both systems (Linux and Windows 10)? > Any precautions concerning the ownership etc. of the host system? > > > > Am Donnerstag, 22. November 2018 19:47:25 UTC+1 schrieb Eric Deutsch: > > Hi Robert, great, thanks for the testing! Can you elaborate a little on > what the symptoms are here for the file access through the GUI? I think the > file access worked fine in my testing. Maybe one potential fix is setting > some more permissive privileges in the directory you’re mapping into the > --user root container? > > > Run TPP image > > - *Start TPP image:* > docker run -dit --user=root -p 10401:10401 -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data > spctools/tpp > - *Open GUI* with Firefox at > http://localhost:10401/tpp/cgi-bin/tpp_gui.pl > GUI and guest:guest login works! > However: Problems with accessing the directory structure/ uploading > files. > > > > > > *From:* [email protected] <[email protected]> *On > Behalf Of *Robert > *Sent:* Thursday, November 22, 2018 7:11 AM > *To:* spctools-discuss <[email protected]> > *Subject:* [spctools-discuss] Re: Running TPP/Petunia GUI with Docker > > > > The complete Test on Linux 64 bit and Windows 10 > > TPP 5.2 Docker CLI on LinuxSystem and software > > - Docker version 1.13.1, build accfe55-unsupported > - Docker image: docker.io/spctools/tpp ID ebf55696681a > - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM > > Data > > - Reference *data set* from ProteomeXchange repository, identifier > PXD001819 (Journal of Proteomics 132 (2016) 51–62), Orbitrap Velos data of > human standard proteins (UPS Sigma) spiked into yeast background. > - *Conversion of raw data* to .mzML profile, then to .mfg centroid > data using > docker run -it --privileged=true -v > > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast/mzML_profile/:/data > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --mgf > /data/*.mzML > - *Target data base* ups_human_yeast.fasta, composed of : Uniprot *Homo > sapiens* + Uniprot *Saccharomyces cervisiae* + Sigma UPS proteins > sequences > Size of .mgf files: ~700 Mb each, 27 files > FASTA with 33,183 entries > > Start Docker > > # systemctl start docker > 1. Command Line Interface (CLI) > > - *Start TPP docker image* with *mounted data directory*: > docker run -it --privileged=true -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data > spctools/tpp bash > > Run comet PSM search > > - go to data directory data/mgf and *create comet parameters file*: > comet -p > change name to comet.params and edit > database_name = ups_human_yeast.fasta > decoy_search = 1 > - Start comet search: > time comet *.mgf > time real 28m45.053s, ~1min/sample, ~140 Mb/sample > > Run PeptideProphet > > - in the directory of comet .pep.xml results run: for i in *.pep.xml; > do PeptideProphetParser $i; done > ~15 s/sample, ~80 Mb/sample > > Run ProteinProphet > > - in the directory of PeptideProphet .pep.xml results run: for i in > *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done > ~3 s/sample, ~7 Mb/sample > > 2. Petunia GUI session (on Linux 64 bit)System and software > > - Docker version 1.13.1, build accfe55-unsupported > - Docker image: docker.io/spctools/tpp ID ebf55696681a > - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM > > Run TPP image > > - *Start TPP image:* > docker run -dit --user=root -p 10401:10401 -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data > spctools/tpp > - *Open GUI* with Firefox at > http://localhost:10401/tpp/cgi-bin/tpp_gui.pl > GUI and guest:guest login works! > However: Problems with accessing the directory structure/ uploading > files. > > TPP 5.2 Docker CLI on WindowsSystem and software > > - Docker version 18.06.1-ce, build e68fc7a > - Docker image: docker.io/spctools/tpp ID ebf55696681a > - running on OS Name Microsoft Windows 10 Enterprise, Processor Intel® > Core™ i5-3470S CPU @ 2.90GHz, 2901 Mhz, 4 Core(s), 4 Logical Processor(s), > 8 Gb RAM > > Data > > - *MS/MS data* from Waters Synapt DDA experiments, exported to .mgf > (see below). 2 samples with ~400 Mb each. > - *FASTA database* composed from EST database and Uniref50 plants, > created by > cat db_1.fasta db_2.fasta > uni50plantsplus.fasta, 3,557,556 entries. > Data set not public yet (sorry). > > Convert Waters Synapt data to mgf > > · load msconvert image with vendor libraries: docker run -it -v > C:\TPP\data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses bash > > · dive into data directory and run with LockMass Filter: > wine msconvert --filt "lockmassRefiner mz=785.8426" --mgf *.raw > > · exit image by exit. > > · *Start TPP* docker session: > docker run -it -v C:\TPP\data:/data spctools/tpp bash > Comet PSM search > > - use comet.params from above, just change database_name = > uni50plantsplus.fasta > - with .mgf files, .fasta sequence database and comet.params in the > same directory, run: > time comet *.mgf Load spectra killed; change in comet.params: > spectrum_batch_size > = 1000 > > Run PeptideProphet > > - in the directory of comet .pep.xml results run: for i in *.pep.xml; > do PeptideProphetParser $i; done > > Run ProteinProphet > > - in the directory of PeptideProphet .pep.xml results run: for i in > *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done > > Convert prot.xml to HTML/EXCEL > > - In the directory of .prot.xml data run: > for i in *.prot.xml; do /usr/local/tpp/cgi-bin/ProtXMLViewer.pl -file > $i -action ExportExcel; done > Leave TPP docker session by exit and enjoy your results. > > Conclusion > > The TPP docker image ebf55696681a (version 5.2) runs on both, Linux and > Windows 10 host, in the CLI mode as expected. > > > > > > Am Freitag, 16. November 2018 16:39:06 UTC+1 schrieb Robert: > > TPP 5.2 Docker on Linux > > # System and software > > - Docker version 1.13.1, build accfe55-unsupported > - Docker image: docker.io/spctools/tpp ID ebf55696681a > - running on Fedora 29, Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz, 16 Gb > RAM > > # Data > > - Reference **data set** from ProteomeXchange repository, identifier > PXD001819 (Journal of Proteomics 132 (2016) 51–62), Orbitrap Velos data of > human standard proteins (UPS Sigma) spiked into yeast background. > - **Conversion of raw data** to .mzML profile, then to ``.mfg`` centroid > data using > ``docker run -it --privileged=true -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast/mzML_profile/:/data > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --mgf > /data/*.mzML`` > - **Target data base** ``ups_human_yeast.fasta``, composed of : Uniprot > _Homo sapiens_ + Uniprot _Saccharomyces cervisiae_ + Sigma UPS proteins > sequences > Size of .mgf files: ~700 Mb each, 27 files > FASTA with 33183 entries > > # Start Docker > ``# systemctl start docker`` > > # 1. Command Line Interface (CLI) > - **Start TPP docker image** with **mounted data directory**: > ``docker run -it --privileged=true -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data > spctools/tpp bash `` > > ## Run comet PSM search > > - go to data directory data/mgf and **create comet parameters file**: > ``comet -p`` > change name to comet.params and edit > ``database_name = ups_human_yeast.fasta > decoy_search = 1`` > - Start comet search: > ``time comet *.mgf`` > time real 28m45.053s, ~1min/sample, ~140 Mb/sample > > ## Run PeptideProphet > > - in the directory of comet .pep.xml results run: > ``for i in *.pep.xml; do PeptideProphetParser $i; done`` > ~15 s/sample, ~80 Mb/sample > > ## Run ProteinProphet > > - in the directory of PeptideProphet .pep.xml results run: > ``for i in *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done`` > ~3 s/sample, ~7 Mb/sample > > ## Convert to HTML/EXCEL > > ``pepxml2html`` not found. > Leaving TPP docker session by ``exit``. > - Conversion with own script < > https://bitbucket.org/lababi/protyquant/src/06deaeb70a09b8121ce0adc1d7d6da389afe7175/python-scripts/protxml_to_tsv.py?at=master>: > > > ``for i in *.prot.xml; do python3 protxml_to_tsv.py $i; done`` > > # 2. Petunia GUI session > > - **Start TPP image:** > ``docker run -dit --user=root -p 10401:10401 -v > /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data > spctools/tpp`` > - **Open GUI** with Firefox at < > http://localhost:10401/tpp/cgi-bin/tpp_gui.pl> > GUI and guest:guest login works! > However: Problems with accessing the directory structure/ uploading files. > > > > > > Am Montag, 22. Oktober 2018 14:49:30 UTC+2 schrieb Robert: > > Dear TPP friends, > > has anyone tried (or even solved) to run the TPP/Petunia GUI from a Docker > container/image? > > Best, Robert > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
