Release v0.8.6

Author: pjotrp

README.md

@@ -54,8 +54,8 @@ configurations. Here are some comparison
 [metrics](https://public-docs.crg.es/rguigo/Data/epalumbo/sambamba_ws_report.html). For
 example for flagstat sambamba is 1.4x faster than samtools. For index
 they are similar. For Markdup almost 6x faster and for view 4x
-faster. For sort sambamba has been beaten generally, though sambamba
-is up to 2x faster on large RAM machines.
+faster. For sort sambamba has been beaten, though sambamba is up to 2x
+faster than samtools on large RAM machines (120GB+).
 
 In addition sambamba has a few interesting features to offer, in particular
 
@@ -79,7 +79,7 @@ Sambamba is free and open source software, licensed under GPLv2+.
 See manual pages [online](https://lomereiter.github.io/sambamba/docs/sambamba-view.html)
 to know more about what is available and how to use it.
 
-For more information on Sambamba contact the mailing list (see below).
+For more information on Sambamba contact the mailing list (see [Getting help](#getting-help)).
 
 <a name="install"></a>
 # Binary installation
@@ -90,7 +90,7 @@ are Github source and binary
 [releases](https://github.com/biod/sambamba/releases). Simply download
 the tarball, unpack it and run it. For example
 
-```sh
+```bash
 wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba_v0.6.8_linux.tar.bz2
 tar xvjf sambamba_v0.6.8_linux.tar.bz2
 ./sambamba_v0.6.8
@@ -116,13 +116,12 @@ A [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for samb
 
 ## Debian GNU/Linux install
 
-Debian: see Debian packages.
+Debian: see [Debian packages](https://tracker.debian.org/pkg/sambamba).
 
 ## Homebrew install
 
 Users of Homebrew can also use the formula from `homebrew-science`.
 
-
 <a name="help"></a>
 # Getting help
 
@@ -180,16 +179,7 @@ which targets LLVM. LLVM versions 6 is faster than earlier editions.
 
 ## Compilation dependencies
 
-- git (to check out the repo)
-- gcc compiler 4.9 or later (for htslib)
-- D compiler 1.7.0 or later (ldc2, see below)
-- python2 (parses D-compiler header for version info)
-- zlib (library)
-- lz4 (library)
-- htslib (submodule)
-- BioD (source)
-- undeaD (source)
-- python2
+See [INSTALL.md](./INSTALL.md).
 
 ## Compiling for Linux
 
@@ -224,6 +214,8 @@ you can run
 make check
 ```
 
+See also [INSTALL.md](./INSTALL.md).
+
 ### GNU Guix
 
 To build sambamba the LDC compiler is also available in GNU Guix:
@@ -234,14 +226,13 @@ guix package -i ldc
 
 ## Compiling for Mac OS X
 
-Note: the Makefile does not work. Someone want to fix that using the
-Makefile.old version? See also https://github.com/biod/sambamba/issues/338.
+Sambamba builds on MacOS. We have a Travis [integration test](https://travis-ci.org/pjotrp/sambamba) as
+an example. It can be something like
 
 ```sh
     brew install ldc
     git clone --recursive https://github.com/biod/sambamba.git
     cd sambamba
-    git clone https://github.com/dlang/undeaD
     make
 ```
 
@@ -253,6 +244,7 @@ documentation can be found in the source code and the [development
 documentation](https://github.com/biod/sambamba-dev-docs).
 
 <a name="debug"></a>
+
 # Debugging and troubleshooting
 
 ## Segfaults on certain Intel Xeons

RELEASE-NOTES.md

@@ -1,12 +1,12 @@
-## ChangeLog v0.6.8 (20181003)
+## ChangeLog v0.6.8 (20181004)
 
 Pre-release with a much faster statically compiled binary. 10-20%
 faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed
 regression of v0.6.7 for large files due to singleobj compilation. See
 also #345 and
 [performance](https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org)
 
-64-bit compilation should be fine on ldc 1.10. i386 target is still a problem.
+64-bit compilation should be fine on ldc 1.10+. i386 target is still a problem.
 
 + Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)
 + Fix missing PM tag in #356 (thanks Kurt Hetrick @Kurt-Hetrick)
@@ -28,3 +28,52 @@ also #345 and
 + Added shunit2 to the source tree for testing
 + Update python build dependencies to use python3.x
 + Fixed a number of D compiler messages on deprecated features (ldc 1.11)
+
+To install the image, download and
+
+```sh
+md5sum sambamba-0.6.8.gz
+25efb5604ae5fe7c750e8020326787c5  sambamba-0.8.6.gz
+gzip -d sambamba-0.6.8.gz
+chmod a+x sambamba-0.6.8
+
+./sambamba-0.8.6
+
+sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
+    LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
+```
+
+The binary images were reproducibly built on x86_64 with
+
+```sh
+~/.config/guix/current/bin/guix pull -l
+Generation 3    Sep 25 2018 09:39:08
+  guix 932839f
+    repository URL: https://git.savannah.gnu.org/git/guix.git
+    branch: origin/master
+    commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
+
+
+guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
+make clean && make -j 16 && make check
+
+for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
+/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread-2.27.so
+/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm-2.27.so
+/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/librt-2.27.so
+/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libdl-2.27.so
+/gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1
+/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so
+# build static image
+make clean && make release -j 16 && make check
+```
+
+Git submodule versions were
+
+```
+ git submodule status
+ 2f0634b187e0f454809432093238cf31e9fbfee6 BioD (v0.2.0-5-g2f0634b)
+ 2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5 htslib (0.2.0-rc10-271-g2f3c3ea)
+ b3692db46d2b23a7c0af2d5e69988c94f126e10a lz4 (v1.8.2)
+ 9be93876982b5f14fcca60832563b3cd767dd84d undeaD (v1.0.1-49-g9be9387)
+ ```