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 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]/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 Windows
> > > System 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
> > > --
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