Andreas Tille pushed to branch master at Debian Med / sortmerna
Commits: f0961581 by Andreas Tille at 2022-02-01T13:39:11+01:00 Sort out documentation - - - - - d9b2d7ff by Andreas Tille at 2022-02-01T15:31:57+01:00 Sort out doc installation (some of the docs are not part of upstream tarball any more) - - - - - 5 changed files: - debian/README_scripts.txt → debian/README.Debian - − debian/doc-base - debian/docs - debian/install - debian/rules Changes: ===================================== debian/README_scripts.txt → debian/README.Debian ===================================== @@ -1,9 +1,13 @@ +sortmerna for Debian +==================== + The Debian package does not come with the large reference files needed to run the pipeline but they can be fetched easily by running the following: $ sudo /usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh -These files can also be recreated from the original sources. The following -instructions are provided with the original source release of SortMeRNA: - +These files can also be recreated from the original sources. The +instructions are provided with the original source release of SortMeRNA +(see README.md) + -- Andreas Tille <[email protected]> Mon, 31 Jan 2022 13:37:04 +0100 ===================================== debian/doc-base deleted ===================================== @@ -1,20 +0,0 @@ -Document: sortmerna -Title: SortMeRNA User Manual -Author: Evguenia Kopylova <[email protected]> -Abstract: tool for filtering, mapping and OTU-picking NGS reads - SortMeRNA is a biological sequence analysis tool for filtering, mapping and - OTU-picking NGS reads. The core algorithm is based on approximate seeds and - allows for fast and sensitive analyses of nucleotide sequences. The main - application of SortMeRNA is filtering rRNA from metatranscriptomic data.. - Additional applications include OTU-picking and taxonomy assignation available - through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). - SortMeRNA takes as input a file of reads (fasta or fastq format) and one or - multiple rRNA database file(s), and sorts apart rRNA and rejected reads into - two files specified by the user. Optionally, it can provide high quality local - alignments of rRNA reads against the rRNA database. SortMeRNA works with - Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and - BLAST-like alignments. -Section: Science/Biology - -Format: pdf -Files: /usr/share/doc/sortmerna/SortMeRNA-User-Manual-2.1.pdf ===================================== debian/docs ===================================== @@ -1 +1,2 @@ -*.pdf +AUTHORS +README* ===================================== debian/install ===================================== @@ -1,6 +1,3 @@ scripts /usr/share/sortmerna debian/scripts/* /usr/share/sortmerna/rRNA_databases/scripts -rRNA_databases/scripts/* /usr/share/sortmerna/rRNA_databases/scripts -tmp/README.txt /usr/share/sortmerna/rRNA_databases -sortmerna /usr/bin -indexdb_rna /usr/bin +# obj-*/src/sortmerna/sortmerna /usr/bin ===================================== debian/rules ===================================== @@ -10,28 +10,9 @@ export CMAKE_PREFIX_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)/cmake/ %: dh $@ -#override_dh_auto_configure: -# dh_auto_configure -- --includedir=/usr/include/sortmerna - override_dh_clean: dh_clean rm -f include/memcheck.h - rm -rf tmp - -override_dh_auto_build: - dh_auto_build - mkdir -p tmp - cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt - -# Uses old interface of skbio (see README.source) -#override_dh_auto_test: -#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) -# python3 ./tests/test_sortmerna.py -#endif - -override_dh_auto_install: - #Skip this - do it manually - true override_dh_fixperms: dh_fixperms View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/5dec8d9ba46763d3e40f04a3cfcadcea16b6008e...d9b2d7ff6ebf068b5cffc7a147d580a84ef53a1e -- View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/5dec8d9ba46763d3e40f04a3cfcadcea16b6008e...d9b2d7ff6ebf068b5cffc7a147d580a84ef53a1e You're receiving this email because of your account on salsa.debian.org.
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