New Upstream Snapshot - sortmerna

Ready changes

Summary

Merged new upstream version: 4.3.6+git20221026.1.2ac819a (was: 4.3.6).

Resulting package

Built on 2023-01-07T17:23 (took 19m30s)

The resulting binary packages can be installed (if you have the apt repository enabled) by running one of: 

apt install -t fresh-snapshots sortmerna-dbgsymapt install -t fresh-snapshots sortmerna

Lintian Result

Diff

diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index f787daf..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,13 +0,0 @@
-*.a
-*.o
-*~
-*.dylib
-.deps
-.dirstamp
-/autom4te.cache
-/config.h
-/config.log
-/config.status
-/stamp-h1
-Makefile
-Makefile.in
diff --git a/README.md b/README.md
index 29e0b5e..806edae 100644
--- a/README.md
+++ b/README.md
@@ -7,9 +7,11 @@ SortMeRNA is a local sequence alignment tool for filtering, mapping and clusteri
 The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads.
 The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.
 SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple
-rRNA database file(s), and sorts apart aligned and rejected reads into two files.
-Additional applications include clustering and taxonomy assignation available through [QIIME v1.9.1](http://qiime.org). SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and
-BLAST-like alignments.
+rRNA database file(s), and sorts apart aligned and rejected reads into two files. SortMeRNA works
+with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
+
+SortMeRNA is also available through [QIIME v1.9.1](http://qiime.org) and
+the [nf-core RNA-Seq pipeline v.3.9](https://nf-co.re/rnaseq/3.9).
 
 # Table of Contents
 
@@ -134,9 +136,9 @@ sortmerna --ref REF_PATH_1 --ref REF_PATH_2 --ref REF_PATH_3 --reads READS_PATH_
 
 ```
 
-More examples can be found in [test.jinja.yaml](https://github.com/biocore/sortmerna/blob/master/scripts/test.jinja.yaml) and [run.py](https://github.com/biocore/sortmerna/blob/master/scripts/run.py)
+More examples can be found in [test.jinja](https://github.com/biocore/sortmerna/blob/master/scripts/test.jinja) and [run.py](https://github.com/biocore/sortmerna/blob/master/scripts/run.py)
 
-Refer to the [Manual](https://github.com/biocore/sortmerna/wiki/2.-User-manual-(todo)) for usage details
+Refer to the [Manual](https://sortmerna.readthedocs.io/en/latest/) for usage details
 
 ### Execution trace
 
diff --git a/debian/changelog b/debian/changelog
index 66400e0..ac4364d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,14 @@
-sortmerna (4.3.6-3) UNRELEASED; urgency=medium
+sortmerna (4.3.6+git20221026.1.2ac819a-1) UNRELEASED; urgency=medium
 
+  [ Étienne Mollier ]
   * d/rules: convert example files to Unicode per lintian flag.
   * typos.patch: add; fix typos caught by lintian.
   * d/copyright: update copyright year.
 
- -- Étienne Mollier <emollier@debian.org>  Sat, 07 Jan 2023 17:42:57 +0100
+  [ Debian Janitor ]
+  * New upstream snapshot.
+
+ -- Étienne Mollier <emollier@debian.org>  Sat, 07 Jan 2023 17:16:32 -0000
 
 sortmerna (4.3.6-2) unstable; urgency=medium
 
diff --git a/debian/patches/cmake_RocksDB.patch b/debian/patches/cmake_RocksDB.patch
index 24d420f..7235316 100644
--- a/debian/patches/cmake_RocksDB.patch
+++ b/debian/patches/cmake_RocksDB.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 31 Jan 2022 13:37:04 +0100
 Description: Fix finding RocksDB
 
---- a/src/sortmerna/CMakeLists.txt
-+++ b/src/sortmerna/CMakeLists.txt
+Index: sortmerna.git/src/sortmerna/CMakeLists.txt
+===================================================================
+--- sortmerna.git.orig/src/sortmerna/CMakeLists.txt
++++ sortmerna.git/src/sortmerna/CMakeLists.txt
 @@ -12,10 +12,7 @@ set(CMAKE_CXX_STANDARD 17)
  
  find_package(Threads REQUIRED)
diff --git a/debian/patches/concurrentqueue.h.patch b/debian/patches/concurrentqueue.h.patch
index b18c4f6..f39876c 100644
--- a/debian/patches/concurrentqueue.h.patch
+++ b/debian/patches/concurrentqueue.h.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 31 Jan 2022 13:37:04 +0100
 Description: Fix include statement for Debian packaged concurrentqueue
 
---- a/include/readsqueue.hpp
-+++ b/include/readsqueue.hpp
+Index: sortmerna.git/include/readsqueue.hpp
+===================================================================
+--- sortmerna.git.orig/include/readsqueue.hpp
++++ sortmerna.git/include/readsqueue.hpp
 @@ -46,7 +46,7 @@
  #include "read.hpp"
  
diff --git a/debian/patches/no_static_linking.patch b/debian/patches/no_static_linking.patch
index f025de1..94c721a 100644
--- a/debian/patches/no_static_linking.patch
+++ b/debian/patches/no_static_linking.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 31 Jan 2022 13:37:04 +0100
 Description: Prevent static linking
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
+Index: sortmerna.git/CMakeLists.txt
+===================================================================
+--- sortmerna.git.orig/CMakeLists.txt
++++ sortmerna.git/CMakeLists.txt
 @@ -69,10 +69,10 @@ set(CONCURRENTQUEUE_URL https://github.c
  set(CONCURRENTQUEUE_HOME ${EXTERNAL_DEPS}/concurrentqueue CACHE PATH "Concurrent queue library installation directory")
  #set(gflags_DIR  ${EXTERNAL_DEPS}/gflags/dist/lib/cmake/gflags CACHE PATH "GFlags library configuration")
diff --git a/debian/patches/rapidjson.patch b/debian/patches/rapidjson.patch
index 23e40b0..b27e003 100644
--- a/debian/patches/rapidjson.patch
+++ b/debian/patches/rapidjson.patch
@@ -4,8 +4,10 @@ Description: Remove upstream RapidJson module
 Author: Mathieu Malaterre <malat@debian.org>
 Last-Update: 2022-01-31
 
---- a/src/sortmerna/CMakeLists.txt
-+++ b/src/sortmerna/CMakeLists.txt
+Index: sortmerna.git/src/sortmerna/CMakeLists.txt
+===================================================================
+--- sortmerna.git.orig/src/sortmerna/CMakeLists.txt
++++ sortmerna.git/src/sortmerna/CMakeLists.txt
 @@ -68,9 +68,7 @@ include(FindZLIB)
  # prevent CONFIG search mode
  find_package(ZLIB MODULE REQUIRED)
diff --git a/debian/patches/typos.patch b/debian/patches/typos.patch
index 727c638..009c3c5 100644
--- a/debian/patches/typos.patch
+++ b/debian/patches/typos.patch
@@ -4,9 +4,11 @@ Forwarded: no
 Last-Update: 2023-01-07
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- sortmerna.orig/3rdparty/cmph/brz.c
-+++ sortmerna/3rdparty/cmph/brz.c
-@@ -152,7 +152,7 @@
+Index: sortmerna.git/3rdparty/cmph/brz.c
+===================================================================
+--- sortmerna.git.orig/3rdparty/cmph/brz.c
++++ sortmerna.git/3rdparty/cmph/brz.c
+@@ -152,7 +152,7 @@ cmph_t *brz_new(cmph_config_t *mph, doub
  	// Clustering the keys by graph id.
  	if (mph->verbosity)
  	{
@@ -15,8 +17,10 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  	}
  
  	while(1)
---- sortmerna.orig/ChangeLog
-+++ sortmerna/ChangeLog
+Index: sortmerna.git/ChangeLog
+===================================================================
+--- sortmerna.git.orig/ChangeLog
++++ sortmerna.git/ChangeLog
 @@ -47,7 +47,7 @@
  15 August 2014
  	- [affects Installation] added script `build.sh` to call configure, touch commands and make in order to avoid timestamp issues when cloning this repository
@@ -26,9 +30,11 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  
  	(a) —best 1, the s_align array is size 1 and only the single best alignment is stored, being the first encountered alignment if multiple alignments of equal score are found.
  	(b) —best 4, the s_align array is size 4. Assume the first 2 alignments score 144 (occupying the first 2 slots on s_align array) and the next 3 alignments score 197 (2 of these alignments will occupy the final 2 slots, where the 3rd alignment will overwrite the first slot holding 144). We will have a situation like: 197, 144, 197, 197. In order to follow the same principle of (a) where the first encountered alignment of the highest score is output, we need to know that this alignment was in slot 3 (not slot 1).
---- sortmerna.orig/include/options.hpp
-+++ sortmerna/include/options.hpp
-@@ -121,7 +121,7 @@
+Index: sortmerna.git/include/options.hpp
+===================================================================
+--- sortmerna.git.orig/include/options.hpp
++++ sortmerna.git/include/options.hpp
+@@ -121,7 +121,7 @@ help_header =
  "  -------------------------------------------------------------------------------------------------------------\n",
  help_ref = 
  	"Reference file (FASTA) absolute or relative path.\n\n"
@@ -37,7 +43,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  help_reads = 
  	"Raw reads file (FASTA/FASTQ/FASTA.GZ/FASTQ.GZ).\n\n"
  	"       Use twice for files with paired reads.\n"
-@@ -198,7 +198,7 @@
+@@ -198,7 +198,7 @@ help_log =
  help_num_alignments = 
  	"Positive integer (INT >=0).\n\n"
  	"       If used with '-" + OPT_NO_BEST + "' reports first INT alignments per read reaching\n"
@@ -46,7 +52,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  	"       Otherwise outputs INT best alignments.\n"
  	"       If INT = 0, all alignments are output\n\n",
  
-@@ -367,7 +367,7 @@
+@@ -367,7 +367,7 @@ help_zip_out =
  	"Controls the output compression                        '-1'\n\n"
  	"       By default the report files are produced in the same format as the input i.e.\n"
  	"       if the reads files are compressed (gz), the output is also compressed.\n"
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..92dd33a
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..83cf06c
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..9f0f80a
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,37 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import sys
+import os
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'sortmerna'
+copyright = '2022, sortmerna development team'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+pygments_style = 'sphinx'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'default'
+try:
+	from better import better_theme_path
+	html_theme_path = [better_theme_path]
+	html_theme = 'better'
+except ImportError:
+	pass
+	
+html_static_path = ['_static']
+html_use_smartypants = True
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..dd4c9f5
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,37 @@
+==========
+User guide
+==========
+
+**SortMeRNA** is a local sequence alignment tool for filtering, mapping and clustering.
+
+.. note::
+   
+   This project is under active development.
+
+Basic usage
+===========
+
+Example 1
+---------
+
+Single reference and single reads file::
+
+   sortmerna --ref REF_PATH --reads READS_PATH
+
+Download latest SortMeRNA databases (v4.3.6)::
+
+   wget https://github.com/biocore/sortmerna/releases/download/v4.3.6/database.tar.gz
+   mkdir rRNA_databases_v4.3.6
+   tar -xvf database.tar.gz -C rRNA_databases_v4.3.6
+
+Download test reads file::
+
+   wget https://github.com/biocore/sortmerna/blob/master/data/test_read.fasta
+
+Run with single reads file::
+
+   sortmerna --ref rRNA_databases_v4.3.6/smr_v4.3_default_db.fasta --reads test_read.fasta
+
+.. note::
+   
+   Index file for ``rRNA_databases_v4.3.6/smr_v4.3_default_db.fasta`` created.

Debdiff

[The following lists of changes regard files as different if they have different names, permissions or owners.]

Files in second set of .debs but not in first

-rw-r--r--  root/root   /usr/lib/debug/.build-id/21/0c4f68ca2f92937db57935a96029a80c45d03a.debug

Files in first set of .debs but not in second

-rw-r--r--  root/root   /usr/lib/debug/.build-id/be/050d9f7b605a857a1b6fb8311df41c5e432da7.debug

Control files of package sortmerna: lines which differ (wdiff format)

  • Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), librocksdb7.8 librocksdb7.7 (>= 7.8.3), 7.7.8), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4)

Control files of package sortmerna-dbgsym: lines which differ (wdiff format)

  • Build-Ids: be050d9f7b605a857a1b6fb8311df41c5e432da7 210c4f68ca2f92937db57935a96029a80c45d03a

More details

Full run details

© 2018-2023 Jelmer Vernooij. File a bug. Source code. Published under the GNU GPLv2 or later.