New upstream version 1.9+dfsg (e36cdb98) · Commits · Debian Med / canu

README.md

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		@@ -11,15 +11,15 @@ Canu is a hierarchical assembly pipeline which runs in four steps:

		## Install:

		The easiest way to get started is to download a [release](http://github.com/marbl/canu/releases).
		* The easiest way to get started is to download a [release](http://github.com/marbl/canu/releases). Installing with a 'package manager' is not encouraged.

		Alternatively, you can also build the latest unreleased from github:
		* Alternatively, you can use the latest unreleased version from the source code. This version has not undergone the same testing as a release and so may have unknown bugs or issues generating sub-optimal assemblies. We recommend the release version for most users.

		git clone https://github.com/marbl/canu.git
		cd canu/src
		make -j <number of threads>

		The unreleased tip has not undergone the same testing as a release and so may have unknown bugs or issues generating sub-optimal assemblies. We recommend the release version for most users.
		* An unsupported Docker image made by Frank Förster is at https://hub.docker.com/r/greatfireball/canu/.

		## Learn:

addCopyrights-BuildData.pl

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		@@ -37,6 +37,7 @@ $stoppingCommits{"64459fe33f97f6d23fe036ba1395743d0cdd03e4"} = 1; # 17 APR 20
		$stoppingCommits{"9e9bd674b705f89817b07ff30067210c2d180f42"} = 1; # 14 AUG 2017
		$stoppingCommits{"0fff8a511fd7d74081d94ff9e0f6c0351650ae2e"} = 1; # 27 FEB 2018 - v1.7
		$stoppingCommits{"fcc3fe19eb635abd735486d215fbf65c56bcf4ee"} = 1; # 22 OCT 2018 - v1.8
		$stoppingCommits{"438412092d4470c63323f20780252b48ec132d44"} = 1; # 04 NOV 2019 - v1.9

		open(F, "< logs") or die "Failed to open 'logs': $!\n";

		@@ -68,6 +69,10 @@ while (!eof(F)) {
		$author = "Brian P. Walenz";
		} elsif (m/koren/i) {
		$author = "Sergey Koren";
		} elsif (m/nurk/i) {
		$author = "Sergey Nurk";
		} elsif (m/rhie/i) {
		$author = "Arang Rhie";
		} else {
		print STDERR "Skipping commit from '$_'\n";
		$author = undef;

addCopyrights.dat

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File changed.

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addCopyrights.pl

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		@@ -226,7 +226,7 @@ my %derived;

		} elsif (m/^D\s+(\S+)\s+(\S+)$/) {
		$authcopy{$1} .= $authcopy{$2}; # Include all authors of old file in new file.
		#$derived{$1} .= $derived{$2};
		$derived{$1} .= $derived{$2};
		$derived{$1} .= "$2\n";

		} else {

buildRelease-DNAnexus.sh

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		#!/bin/sh

		# Generate a script to compile Canu using the Holy Build Box.

		echo > build-linux.sh \#\!/bin/bash
		echo >> build-linux.sh yum install -y git
		echo >> build-linux.sh cd /build/src
		echo >> build-linux.sh gmake -j 12 \> ../Linux-amd64.out 2\>\&1
		echo >> build-linux.sh cd ..
		#echo >> build-linux.sh rm -rf Linux-amd64/obj
		#echo >> build-linux.sh tar -cf canu-linux.Linux-amd64.tar canu-linux/README* canu-linux/Linux-amd64

		chmod 755 build-linux.sh

		echo ""
		echo "-- Build Linux and make tarballs."
		echo ""

		echo "% docker run ..."
		docker run \
		-v `pwd`:/build \
		-t \
		-i \
		--rm phusion/holy-build-box-64:latest /hbb_exe/activate-exec bash /build/build-linux.sh \
		> build-linux.sh.out 2>&1

		rm -f build-linux.sh

		echo ""
		echo "-- Build success?"
		echo ""

		tail -n 1 build-linux.sh.out \| head -n 1
		tail -n 2 Linux-amd64.out \| head -n 1

		# Fetch the Upload Agent and install in our bin/.

		if [ ! -e src/pipelines/dx-canu/resources/bin/ua ] ; then
		echo ""
		echo "-- Fetch UploadAgent."
		echo ""

		curl -L -R -O https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.31-osx.zip
		curl -L -R -O https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.31-linux.tar.gz

		tar zxf dnanexus-upload-agent-1.5.31-linux.tar.gz

		cp -p dnanexus-upload-agent-1.5.31-linux/ua src/pipelines/dx-canu/resources/bin/
		cp -p dnanexus-upload-agent-1.5.31-linux/ua src/pipelines/dx-trio/resources/bin/

		#rm -rf dnanexus-upload-agent-1.5.31-linux.tar.gz
		rm -rf dnanexus-upload-agent-1.5.31-linux
		fi

		# Remove the old app.

		echo ""
		echo "-- Purge previous dx-canu and dx-trio builds."
		echo ""

		echo "% rm -rf dx-canu/ dx-trio/"
		rm -rf dx-canu/ dx-trio/
		mkdir -p dx-canu/ dx-trio/
		mkdir -p dx-canu/resources/bin/ dx-trio/resources/bin/
		mkdir -p dx-canu/resources/usr/bin/ dx-trio/resources/usr/bin/
		mkdir -p dx-canu/resources/usr/lib/ dx-trio/resources/usr/lib/
		mkdir -p dx-canu/resources/usr/share/ dx-trio/resources/usr/share/

		# Package all that up into dx-canu.

		echo ""
		echo "-- Package new bits into dx-canu and dx-trio builds."
		echo ""

		echo "% rsync ..."
		rsync -a src/pipelines/dx-canu/ dx-canu/
		rsync -a Linux-amd64/bin/ dx-canu/resources/usr/bin/
		rsync -a Linux-amd64/lib/ dx-canu/resources/usr/lib/
		rsync -a Linux-amd64/share/ dx-canu/resources/usr/share/

		rsync -a src/pipelines/dx-trio/ dx-trio/
		rsync -a Linux-amd64/bin/ dx-trio/resources/usr/bin/
		rsync -a Linux-amd64/lib/ dx-trio/resources/usr/lib/
		rsync -a Linux-amd64/share/ dx-trio/resources/usr/share/

		#rm -fr Linux-amd64/obj Linux-amd64.tar Linux-amd64.tar.gz
		#tar -cf Linux-amd64.tar Linux-amd64
		#gzip -1v Linux-amd64.tar
		#dx rm Linux-amd64.tar.gz
		#dx upload Linux-amd64.tar.gz

		echo ""
		echo "-- Build the DNAnexus apps."
		echo ""

		echo "% dx build -f dx-canu"
		dx build -f dx-canu

		echo "% dx build -f dx-trio"
		dx build -f dx-trio

		exit 0