samtools dependency

[mojaveazure]

samtools dependency

[mojaveazure]

Searching for SAMTools in brew gives me this:

hoffmanp$ brew search samtools
homebrew/science/samtools                homebrew/science/samtools-0.1 

If I want to install SAMTools using brew:

hoffmanp$ brew install samtools
==> Installing samtools from homebrew/science
==> Downloading https://github.com/samtools/samtools/archive/1.2.tar.gz
==> Downloading from https://codeload.github.com/samtools/samtools/tar.gz/1.2
######################################################################## 100.0%
==> make HTSDIR=/usr/local/opt/htslib/include HTSLIB=/usr/local/opt/htslib/lib/l
🍺  /usr/local/Cellar/samtools/1.2: 44 files, 1M, built in 18 seconds
hoffmanp$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)

Usage:   samtools <command> [options]

Commands:
  -- indexing
         faidx       index/extract FASTA
         index       index alignment
  -- editing
         calmd       recalculate MD/NM tags and '=' bases
         fixmate     fix mate information
         reheader    replace BAM header
         rmdup       remove PCR duplicates
         targetcut   cut fosmid regions (for fosmid pool only)
  -- file operations
         bamshuf     shuffle and group alignments by name
         cat         concatenate BAMs
         merge       merge sorted alignments
         mpileup     multi-way pileup
         sort        sort alignment file
         split       splits a file by read group
         bam2fq      converts a BAM to a FASTQ
  -- stats
         bedcov      read depth per BED region
         depth       compute the depth
         flagstat    simple stats
         idxstats    BAM index stats
         phase       phase heterozygotes
         stats       generate stats (former bamcheck)
  -- viewing
         flags       explain BAM flags
         tview       text alignment viewer
         view        SAM<->BAM<->CRAM conversion

This version works, which is why I say just use brew to install SAMTools. I ran brew update right before I did this, so I have the most recent version of brew on my Mac.

I say in the tutorial to use brew install samtools, as this installs a version of SAMTools that works with ANGSD-wrapper. All Mac commands should work to install ANGSD-wrapper and it's dependencies. I have not included instructions on how to build these packages in a Linux environment, simply because I'm assuming that Linux users know how to install their own software. For those that wish to build SAMTools from source, I point them to the GitHub page, which says "By default, this will build against an HTSlib source tree in ../htslib. You can alter this to a source tree elsewhere or to a previously-installed HTSlib by configuring with --with-htslib=DIR", hence I direct the user to install HTSLib and SAMTools to satisfy this dependency. I re-download HTSLib during the setup routine to make sure ANGSD sees a copy of HTSLib; ANGSD looks for HTSLib in ../htslib, just like SAMTools from source. It does not look for HTSLib in $PATH.

Finally, these are available in most package mangers, which I say on the Installation page. At least, it's available in the Ubuntu/Debian repositories and the Fedora/Red Hat repositories.

I don't think adding a routine to install SAMTools is necessary, but if you have any ideas on how to improve the wiki, I am more than open to suggestions!

[rossibarra]

I would encourage inclusion of default installation of samtools. Some
users will not be linux users but using AW on a cluster and not be super
familiar with linuxy stuff. And the whole point is to make things easy if
possible.

-Jeff

---

Jeffrey Ross-Ibarra

Dept. of Plant Sciences
262 Robbins Hall, Mail Stop 4
University of California
One Shields Ave
Davis, CA 95616

Tel: [phone]
@jrossibarra
www.rilab.org

On Fri, Jan 22, 2016 at 1:57 PM, Paul Hoffman [email protected]
wrote:

Searching for SAMTools in brew gives me this:

hoffmanp$ brew search samtools
homebrew/science/samtools homebrew/science/samtools-0.1

If I want to install SAMTools using brew:

hoffmanp$ brew install samtools
==> Installing samtools from homebrew/science
==> Downloading https://github.com/samtools/samtools/archive/1.2.tar.gz
==> Downloading from https://codeload.github.com/samtools/samtools/tar.gz/1.2######################################################################## 100.0%
==> make HTSDIR=/usr/local/opt/htslib/include HTSLIB=/usr/local/opt/htslib/lib/l
🍺 /usr/local/Cellar/samtools/1.2: 44 files, 1M, built in 18 seconds
hoffmanp$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)

Usage: samtools [options]

Commands:
-- indexing
faidx index/extract FASTA
index index alignment
-- editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
rmdup remove PCR duplicates
targetcut cut fosmid regions (for fosmid pool only)
-- file operations
bamshuf shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
bam2fq converts a BAM to a FASTQ
-- stats
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion

This version works, which is why I say just use brew to install SAMTools.
I ran brew update right before I did this, so I have the most recent
version of brew on my Mac.

I say in the tutorial to use brew install samtools, as this installs a
version of SAMTools that works with ANGSD-wrapper. All Mac commands should
work to install ANGSD-wrapper and it's dependencies. I have not included
instructions on how to build these packages in a Linux environment, simply
because I'm assuming that Linux users know how to install their own
software. For those that wish to build SAMTools from source, I point them
to the GitHub page, which says "By default, this will build against an
HTSlib source tree in ../htslib. You can alter this to a source tree
elsewhere or to a previously-installed HTSlib by configuring with
--with-htslib=DIR", hence I direct the user to install HTSLib and
SAMTools to satisfy this dependency. I re-download HTSLib during the setup
routine to make sure ANGSD sees a copy of HTSLib; ANGSD looks for HTSLib in
../htslib, just like SAMTools from source. It does not look for HTSLib in
$PATH.

Finally, these are available in most package mangers, which I say on the
Installation page. At least, it's available in the Ubuntu/Debian
repositories and the Fedora/Red Hat repositories.

I don't think adding a routine to install SAMTools is necessary, but if
you have any ideas on how to improve the wiki, I am more than open to
suggestions!

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