diff --git a/README b/README index 01467e8334fcae020592f66032ab9b7d01ec01f3..dc504fa3154229f7b7218c435b20171472b53178 100644 --- a/README +++ b/README @@ -72,6 +72,10 @@ Todo list: - Check for os.path.join vulnerabilities. - Use a standard solution for the database migrations in extras/migrations. - Use something like Sphinx to generate development documentation from code. +- There are some problems with the batch architecture, especially that there + cannot be multiple workers without synchronisation problems. + Good read: http://news.ycombinator.com/item?id=3002861 + Suggestion: http://celeryproject.org/ Code style guide: - Follow PEP 8 (code) and PEP 257 (docstrings). diff --git a/extras/cron.d/mutalyzer-mapping-update b/extras/cron.d/mutalyzer-mapping-update index ce361f78953082d23927fff34976057cb5141c8d..cac1a9767741c0a42a372408ac65cb7c58d1647d 100644 --- a/extras/cron.d/mutalyzer-mapping-update +++ b/extras/cron.d/mutalyzer-mapping-update @@ -1,3 +1,5 @@ # Update the mapping database every sunday morning at 03:25 and 04:25 #25 3 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg18 /tmp/seq_gene.md reference -#25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly' +#25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.2/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly' + +##25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly' diff --git a/extras/post-install.sh b/extras/post-install.sh index 4ec0bb71dd427e7acaa81d94ab2f92d490f5b666..466efdde857edc49e97c99d91189179f25dfb3b7 100644 --- a/extras/post-install.sh +++ b/extras/post-install.sh @@ -220,7 +220,8 @@ EOF echo -e "${COLOR_INFO}Populating Mapping table with NCBI data (hg19)${COLOR_END}" # Populate Mapping table with UCSC data (hg19) -wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md +#wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md +wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.2/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md echo -e "${COLOR_INFO}Importing NCBI mapping data, this may take a few minutes (hg19)${COLOR_END}" $($BIN_MAPPING_UPDATE hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly')