Nilesh Patra pushed to branch master at Debian Med / wtdbg2
Commits: 13211a71 by Nilesh Patra at 2020-08-09T14:49:01+00:00 Add autopkgtests - - - - - 8d220b6f by Nilesh Patra at 2020-08-09T14:49:22+00:00 Save up space by not extracting the binary - - - - - 89f01792 by Nilesh Patra at 2020-08-09T14:49:45+00:00 New binary: wtdbg2-examples - - - - - 13b8ea5b by Nilesh Patra at 2020-08-09T14:50:11+00:00 Minor fixes on manpages - - - - - 7b2d763b by Nilesh Patra at 2020-08-09T20:28:05+05:30 Fix spellings - - - - - e56ba773 by Nilesh Patra at 2020-08-09T20:34:28+05:30 Change arch of example binary to all - - - - - 10 changed files: - debian/control - debian/mans/kbm2.1 - debian/mans/wtdbg2.1 - debian/rules - + debian/source/include-binaries - + debian/tests/README - + debian/tests/control - + debian/tests/data/selfSampleData.tar.gz - + debian/tests/run-unit-test - + debian/wtdbg2-examples.docs Changes: ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev Standards-Version: 4.5.0 @@ -19,7 +19,8 @@ Depends: ${shlibs:Depends}, Suggests: ${perl:Depends}, minimap2, samtools, - mummer + mummer, +Recommends: wtdbg2-examples Description: de novo sequence assembler for long noisy reads Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads @@ -34,3 +35,19 @@ Description: de novo sequence assembler for long noisy reads (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and keeps read paths when collapsing k-mers. The use of FBG distinguishes wtdbg2 from the majority of long-read assemblers. + +Package: wtdbg2-examples +Architecture: all +Depends: ${shlibs:Depends}, + ${misc:Depends} +Enhances: wtdbg2 +Description: Examples for wtdbg - de novo sequence assembler + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by + PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads + without error correction and then builds the consensus from intermediate + assembly output. Wtdbg2 is able to assemble the human and even the 32Gb + Axolotl genome at a speed tens of times faster than CANU and FALCON + while producing contigs of comparable base accuracy. + . + This package contains a test data set as well as sample scripts + running some test suite provided by Debian also as autopkgtest. ===================================== debian/mans/kbm2.1 ===================================== @@ -56,7 +56,7 @@ Filter low complexity bins (#indexed_kmer less than <\-O>), [2] .TP \fB\-S\fR <float> Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00] -\fB\-S\fR is very useful in saving memeory and speeding up +\fB\-S\fR is very useful in saving memory and speeding up please note that subsampling kmers will have less matched length .TP \fB\-B\fR <int> ===================================== debian/mans/wtdbg2.1 ===================================== @@ -58,7 +58,7 @@ Filter high frequency kmers, maybe repetitive, [1000.05] .TP \fB\-S\fR <float> Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00] -\fB\-S\fR is very useful in saving memeory and speeding up +\fB\-S\fR is very useful in saving memory and speeding up please note that subsampling kmers will have less matched length .TP \fB\-l\fR <float> @@ -178,7 +178,7 @@ Retain dovetail overlaps only, the max overhang size is <\-\-aln\-dovetail>, the .HP \fB\-\-aln\-strand\fR <int> .IP -1: forward, 2: reverse, 3: both. Please don't change the deault vaule 3, unless you exactly know what you are doing +1: forward, 2: reverse, 3: both. Please don't change the deault value 3, unless you exactly know what you are doing .HP \fB\-\-aln\-maxhit\fR <int> .IP @@ -303,7 +303,7 @@ Don't attempt to rescue low coverage edges .HP \fB\-\-node\-min\fR <int> .IP -Min depth of an interval to be selected as valid node. Defaultly, this value is automaticly the same with \fB\-\-edge\-min\fR. +Min depth of an interval to be selected as valid node. Defaultly, this value is automatically the same with \fB\-\-edge\-min\fR. .HP \fB\-\-node\-max\fR <int> .IP @@ -364,7 +364,7 @@ Min length of contigs to be output, 5000 .HP \fB\-\-ctg\-min\-nodes\fR <int> .IP -Min num of nodes in a contig to be ouput, 3 +Min num of nodes in a contig to be output, 3 .HP \fB\-\-minimal\-output\fR .IP ===================================== debian/rules ===================================== @@ -19,6 +19,12 @@ libexecdir=$(prefix)/lib/$(DEB_SOURCE) dh $@ override_dh_auto_build: + sed -i 's/\/usr\/bin\/env perl/\/usr\/bin\/perl/' scripts/* + sed -i 's/memeory/memory/' *.c *.h *.md + sed -i 's/automaticly/automatically/' *.c + sed -i 's/ouput/output/' *.c + sed -i 's/vaule/value/' *.c + sed -i 's/annonymous/anonymous/' *.h ifeq (amd64,$(DEB_HOST_ARCH)) mkdir -p $(prefix) mkdir -p $(libexecdir) ===================================== debian/source/include-binaries ===================================== @@ -0,0 +1 @@ +debian/tests/data/selfSampleData.tar.gz ===================================== debian/tests/README ===================================== @@ -0,0 +1,5 @@ +Tests for wtdbg2 +================= + +The data for tests has been referenced from: + http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz ===================================== debian/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @, bwa, minimap2, samtools +Restrictions: allow-stderr + ===================================== debian/tests/data/selfSampleData.tar.gz ===================================== Binary files /dev/null and b/debian/tests/data/selfSampleData.tar.gz differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,43 @@ +#!/bin/bash +set -e + +pkg=wtdbg2 + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp /usr/share/doc/${pkg}-examples/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * +tar -xvf *.tar +cd selfSampleData + +# Checks whether file checksum is same as expected +function check_same() +{ + # $1 : file name + # $2 : checksum value + [ "$(cat $1 | md5sum | awk '{print $1}')" == $2 ] || exit 1 +} + +echo "Begin Execution" +wtdbg2 -t 16 -x rs -g 4.6m -o dbg pacbio_filtered.fastq + +# Step by step commandlines +# assemble long reads +wtdbg2 -x rs -g 4.6m -i pacbio_filtered.fastq -t 16 -fo dbg + +# derive consensus +wtpoa-cns -t 16 -i dbg.ctg.lay.gz -fo dbg.raw.fa +check_same dbg.raw.fa a2c479242d7c6ad6c8ffd979b821aa01 +echo "PASS" + +# polish consensus, not necessary if you want to polish the assemblies using other tools +minimap2 -t16 -ax map-pb -r2k dbg.raw.fa pacbio_filtered.fastq | samtools sort -@4 >dbg.bam +samtools view -F0x900 dbg.bam | wtpoa-cns -t 16 -d dbg.raw.fa -i - -fo dbg.cns.fa +check_same dbg.cns.fa 62a41e5cb7a5e702523237f4ab65c376 +echo "PASS" + ===================================== debian/wtdbg2-examples.docs ===================================== @@ -0,0 +1 @@ +debian/tests/data/* View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2 -- View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
