Of course! Sorry, Eric! Petunia runs on http://localhost:10401/tpp/cgi-bin/tpp_gui.pl, I can login as guest, but I cannot upload data/ create directories.
docker run -dit *--user=root* -p 10401:10401 -v */tmp/tpp*:/data spctools/tpp apache2ctl -DFOREGROUND In Petunia: /data/ "Set as Working Directory" ups_yeast "Create new directory" => - ERROR: creating the folder "/data/ups_yeast":Permission denied If I choose a file and try to upload it: => - File open error: Permission denied Theoretically, anyone should be able to read and write this directory: [root@localhost tpp]# ls -al total 0 drwxrwxrwx. 2 root root 40 10. Dez 10:53 . drwxrwxrwt. 28 root root 840 10. Dez 11:04 .. Even, if I move files manually to this directory, they are not seen by Petunia. I also tried to mount (-v) a user directory, which works with the CLI session, but not with Petunia. Someone (docker, apache, .. ??) seems to have missing privileges, even if I started the container as user root. Best, Robert Am Sonntag, 9. Dezember 2018 19:12:18 UTC+1 schrieb Eric Deutsch: > > Hi Robert, I think you just need to go here: > > http://myhost:10401/tpp/cgi-bin/tpp_gui.pl > > > > instead of here: > > http://myhost:10401/ > > > > ? Could that be it? > > > > Thanks, > > Eric > > > > > > *From:* spctools...@googlegroups.com <javascript:> < > spctools...@googlegroups.com <javascript:>> *On Behalf Of *Robert Winkler > *Sent:* Thursday, December 6, 2018 10:28 PM > *To:* spctools...@googlegroups.com <javascript:> > *Cc:* spctools...@googlegroups.com <javascript:> > *Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker > > > > Hi Eric, > > > > The port 10401 works fine. However, there is no Petunia showing up. When > calling http://localhost:10401/ from the Firefox Browser the "Apache2 > Ubuntu Default Page" appears. The host system is Fedora 29. > > > > To me it seems like a problem in the Apache2 configuration. > > > > This is a summary of what I did (I also tested other ports, mounted > directories etc.): > > > > #docker system prune --all --force > > > > #docker run -dit --user=root -p 10401:10401 -v > /home/robertwinkler/dataspace/nextcloud/DATA/:/data spctools/tpp apache2ctl > -DFOREGROUND > > f1ad3670f4f7117db97c9cff8061a95df718c748e348660a0ca1c78818a0e848 > > > > # docker ps > > CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES > > f1ad3670f4f7 spctools/tpp "apache2ctl -DFORE..." 23 minutes ago Up 23 > minutes 0.0.0.0:10401->10401/tcp quizzical_bhabha > > > > # docker images > > REPOSITORY TAG IMAGE ID CREATED SIZE > > docker.io/spctools/tpp latest 73727a87cff0 8 days ago 2.86 GB > > > > Best, Robert > > > > On Dec 3 2018, at 6:29 pm, Eric Deutsch <edeu...@systemsbiology.org > <javascript:>> wrote: > > Hi Robert, when you get an error like this: > > > > > > > > Bind for 0.0.0.0:10401 > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/0?redirect=http%3A%2F%2F0.0.0.0%3A10401&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > failed: port is already allocated > > > > > > > > That means that there is already an Apache service listening on the 10401 > point on the Docker **host** machine. The first thing to consider is > there perhaps already another container running on 10401. Maybe you don’t > need to start another container because it’s already running. Based on the > your `docker ps` it looks like this is your issue. Maybe you don’t need to > launch another TPP? Or maybe you would want to shut down that older > container before launching a new one? > > > > > > > > Or it’s possible that you already have TPP installed and running on the > machine that is the Docker host. If that’s the case, you’ll want to map to > a different port so that you can run both at the same time (which is fine), > like this: > > > > > > > > sudo docker pull spctools/tpp > > > > sudo docker run -dit --user=root -p 10402:10401 -v /tmp/tppdata:/data > spctools/tpp apache2ctl -DFOREGROUND > > > > > > > > Here what I’ve done is bind the local port 10402 to the Apache web server > running in the container. You would then use a web browser to go to: > > > > > > > > http://myhost:10402/tpp/cgi-bin/tpp_gui.pl > > > > > > > > Regards, > > > > Eric > > > > > > > > > > > > *From:* spctools-discuss@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/1?redirect=mailto%3Aspctools-discuss%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > <spctools-discuss@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/2?redirect=mailto%3Aspctools-discuss%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>> > > *On Behalf Of *Robert > > *Sent:* Saturday, December 1, 2018 12:22 AM > > *To:* spctools-discuss <spctools-discuss@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/3?redirect=mailto%3Aspctools-discuss%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > > > *Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker > > > > > > 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 > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/4?redirect=http%3A%2F%2F0.0.0.0%3A10401&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > 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 > > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/5?redirect=http%3A%2F%2Ftools.proteomecenter.org%2Fwiki%2Findex.php%3Ftitle%3DRunning_the_TPP_docker_image&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > > > > > 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:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On > Behalf Of *Robert > > *Sent:* Tuesday, November 27, 2018 3:17 AM > > *To:* spctools-discuss <spctools...@googlegroups.com> > > *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:* spctools...@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/6?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > <spctools...@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/7?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>> > > *On Behalf Of *Robert > > *Sent:* Thursday, November 22, 2018 7:11 AM > > *To:* spctools-discuss <spctools...@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/8?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > > > *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 > > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/9?redirect=http%3A%2F%2Fdocker.io%2Fspctools%2Ftpp&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > 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 > > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/10?redirect=http%3A%2F%2Fdocker.io%2Fspctools%2Ftpp&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > 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 > > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/11?redirect=http%3A%2F%2Fdocker.io%2Fspctools%2Ftpp&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > 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 > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/12?redirect=http%3A%2F%2Fdocker.io%2Fspctools%2Ftpp&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > > 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 > > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/13?redirect=https%3A%2F%2Fbitbucket.org%2Flababi%2Fprotyquant%2Fsrc%2F06deaeb70a09b8121ce0adc1d7d6da389afe7175%2Fpython-scripts%2Fprotxml_to_tsv.py%3Fat%3Dmaster&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > >: > > ``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 spctools-discu...@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/14?redirect=mailto%3Aspctools-discu...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > . > > To post to this group, send email to spctools...@googlegroups.com > <https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/15?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> > . > > Visit this group at 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