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:* [email protected] <[email protected]> *On Behalf Of *Robert Winkler *Sent:* Thursday, December 6, 2018 10:28 PM *To:* [email protected] *Cc:* [email protected] *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 <[email protected]> wrote: Hi Robert, when you get an error like this: Bind for 0.0.0.0:10401 <https://link.getmailspring.com/link/[email protected]/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:* [email protected] <https://link.getmailspring.com/link/[email protected]/1?redirect=mailto%3Aspctools-discuss%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> <[email protected] <https://link.getmailspring.com/link/[email protected]/2?redirect=mailto%3Aspctools-discuss%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>> *On Behalf Of *Robert *Sent:* Saturday, December 1, 2018 12:22 AM *To:* spctools-discuss <[email protected] <https://link.getmailspring.com/link/[email protected]/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/[email protected]/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/[email protected]/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:* [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] <https://link.getmailspring.com/link/[email protected]/6?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> <[email protected] <https://link.getmailspring.com/link/[email protected]/7?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>> *On Behalf Of *Robert *Sent:* Thursday, November 22, 2018 7:11 AM *To:* spctools-discuss <[email protected] <https://link.getmailspring.com/link/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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 [email protected] <https://link.getmailspring.com/link/[email protected]/14?redirect=mailto%3Aspctools-discu...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> . To post to this group, send email to [email protected] <https://link.getmailspring.com/link/[email protected]/15?redirect=mailto%3Aspctools...%40googlegroups.com&recipient=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t> . 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