Martin Mokrejš

Make it clearer what adapters are in the default queries

3

The default queries are TruSeq adapters which is a good default these days with HiSeq/NextSeq datasets. Explain what is the first pair of adapter pairs in the table. It is...

Hi, could johnny provide similar functionality to https://7thzero.com/blog/certificate-password-recovery-tool ? For testing, let's take any current passhphrase you have, discard first leading 8 chars and provide the remaining portion of the...

abyss-2.1.0: cannot enable sparsehash due to gcc-5.4.0 with gomp

10

Hi, I am trying older gcc versions and I received: ``` checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability......

Cleanup Makefile to respect users environment.

1

Respect variables already defined and support temporary path $(DESTDIR) to install into.

bowtie2 does not insert TABs into RG line

7

Hi, I am using bowtie 2.3.5.1 and try to get sample and other IDs recorded on the `@RG` line. Unfortunately, it seems bowtie2 does not write TABs as separators on...

sci-biology/GFF3toolkit: hint for a new package

8

Something is still broken, please fix it on your own and cherrypick Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Martin Mokrejs

1.6.1: src/core/md5_fingerprint.c:20:10: fatal error: md5.h: No such file or directory

5

Hi, I wanted to update the package for Gentoo Linux from 1.5.10 to 1.6.1 but now it fails with: ``` [compile md5_encoder.o] [compile md5_fingerprint.o] src/core/md5_fingerprint.c:20:10: fatal error: md5.h: No such...

augustus-3.3.2: auxprogs/bam2wig dependencies are incorrect

13

It does not seem one needs any of the following to link: `$(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto`, only `-lbam` is needed.

do not override users compiler and compiler flags use CXX instead CC variable because we need a C++ compiler do not force optimization if user has some CXXFLAGS already in...

Hi, there is http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual but it seems there is no documentation like this in current cd-hit tree (4.6.5). Further, there used to be http://weizhong-lab.ucsd.edu/softwares/cd-hit-454/cdhit-cluster-consensus-2013-03-27.tgz but I don't see it in...