Releases: 0x002A/MuCHSALSA
Releases · 0x002A/MuCHSALSA
Nightly Build
Pipeline improvements (#13) * Exclude temporary/generated files of pipeline as well as editor swap files, vagrant data etc. * Set executable bit for pipeline files to fix pipeline death. Make symlink to muchsalsa binary * Reduce cmake version requirement by one subversion to support ubuntu 20.04 LTS (focal) * Added missing dependencies to README.md * Added Vagrantfile to automatically create a virtual build environment. Setup does not yet fully work * Finalized provisioning, vagrant should work as expected now. * Use bioconda jellyfish instead of dnf version * Install quast in vagrant vm * Exclude all dirs starting with build- * Added conda env file including all dependencies. * removed invalid data from conda env * Check number of arguments and print usage in pipeline. Check existence of input files * Consequently use quoting for variables containing paths * Added error handling code to pipeline * Use 40 cores for pipeline. This really should become a cmd line switch ... * Added more quotes around variables in pipeline script * More quotes and allow setting core count from cmd line * Adapt arg count check for 8 args * Added check for availability of required programs to pipeline. * Added commented out code in the scrubber script to work around possible sqlite full disk errors * Use bloom filter mode of abyss instead of legacy mpi mode. Use multi-threading in all supported tools * whitespace fixes * some more quotes in pipeline * .gitignore Qt Creator files * Explicitly ask for python3 in shebang lines of python scripts * pipeline: make symlink of nano reads file in output dir. Prevents race conditions with index creation when running multiple instances in the same directory. Log output is now much more informative, prints individual steps and some more timings.