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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
