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Created with Raphaël 2.2.015Apr6Apr17Dec11Nov30Oct21May1413815Apr9420Mar14131253128Feb262221201817161514131210987Jan28Jun10Apr95438Mar77Feb31Jan3029241619Dec13121187654130Nov2928272116139826Oct1810Aug72131Jul272621Jun31May4Apr23Mar229828Feb27232214Add sorfdb profilemastermasterAdd default psot image for k8sUse new image locationUpdate container imagesFix bug: Feature coordinates are stored as stringsAdd pepstats tool by fabian schneckoIncrease evalue cutoff for bacteria-ecfAdd bias to hmmer domain targetAdd ECF express profileInclude evaule in hmmer result. Use name as fallback if no accession is availableInclude score in ghostx result conversionMerge branch 'develop' of git.computational.bio.uni-giessen.de:SOaAS/psot into developAdd max hits argument to run_ghostx.pyMerge branch 'develop' of git.computational.bio.uni-giessen.de:SOaAS/psot into developImprove targetp json structure by writing out Localization and preserving case of other fields. Also adds a script run execute targetp script quicklyAdd tmhmm to all profilesAdd include_sequence to all profilesAdd profiles for bacteria and eukaryotesFix bug: some ghostx installations output the help page on stderrFix bug: blastp converter ignores sequences without hitsFix bug: hmmer and ghostx don't include sequences with no resultsRedesign databases. Introduce relative database paths. Docker steps mount the associated databases directly.Merge branch 'develop' into containerizationFix docker image locations and database locationsif containerpath is changed in config.yaml, mount point is automatically changed in nextflow.pycleanupdefault_repo again in project directory; error handling in database scriptextended error handling in download_databases_from_s3bucket.sh and cleanup of logfile in main.py happens now if logfile is 1KBpsot deletes all lines except the last ten lines in database_paths.log, if logfile is too big (1MB)databases will be downloaded without testing on availability at the first run; while downloading a lockfile is created to stop other psot instances from downloading at the same timeBUGFIX: config is now loaded while parameter functions are executed, not in the main function anymore; helper scripts are executed in the nextflow script without full path, it was made use of the bin folder in the execution directoryadd fail function to download_databases_from_s3bucket script for error handlingadd download_databases function to main.py, download_databases_from_s3bucket.sh is run as subprocessdatabase directory is written automatically in nextflow config (docker or singularity scope)download_databases_from_s3bucket.sh tests now if folders are misssing in datadir and download only theseadd script 'download_databases_from_s3bucket'Raise exception when profile is not found; Add error propagation to nextflow callbiocontainers are used for blastp and hmmernextflow.config is now generated with docker and singularity scopes in which the local database directory is mounted/bind in the containers to the /databases directory; config.py now concats the right database directory with the database property in regarding modulesrun scripts now print cmdline they used to run and are executed in nextflow.py as subprocesses; analysis tools are now executed in the nextflow processes directly