[med-svn] [Git][med-team/sortmerna][master] 2 commits: Sort out documentation

[Andreas Tille (@tille)]

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 <tille at debian.org>  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 <jenya.kopylov at gmail.com>
-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
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