[MacPorts] #43300: New port request, Stacks, for Next-Gen DNA short-read sequences

[MacPorts]

#43300: New port request, Stacks, for Next-Gen DNA short-read sequences
----------------------+--------------------------------
  Reporter:  pst@…    |      Owner:  macports-tickets@…
      Type:  request  |     Status:  new
  Priority:  Normal   |  Milestone:
 Component:  ports    |    Version:
Resolution:           |   Keywords:
      Port:  stacks   |
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Changes (by macsforever2000@…):

 * cc: pst@… (removed)
 * version:  2.2.1 =>
 * keywords:  NGS, Next Generation Sequencing, DNA =>
 * type:  submission => request
 * port:  Stacks => stacks


Old description:

> HI, I am a geneticist and would love to have "Stacks" ported properly to
> run on Mac OSX. This software enables filtering and alignment of DNA
> sequencing data from next-generation DNA sequencing. It is highly
> needed!!
>
> The performance of Stacks can be improved by installing two external
> libraries. Samtools & Google’s SparseHash. These optional packages must
> be installed and enabled prior to building Stacks. Please make sure that
> these are part of the port (I think these are both part of macports
> already).
> http://samtools.sourceforge.net/
> http://code.google.com/p/sparsehash/
>
> Also, this software is multi-processor aware and GREATLY benefits from
> OpenMP. If this port could make use of OpenMP that would be fantastic! I
> think to do so would require compiling with GCC. Please include OpenMP
> install variants too!!
>
> From the website, it looks like the following are also needed:
> mysql-server php5 apache2
> php-mdb2 php-mdb2-driver-mysql
> libdbd-mysql-perl
> samtools
> libbam-dev
>
> The files and info on the project are located at:
> http://creskolab.uoregon.edu/stacks/
>
> I have attached the latest download. If you need any help testing this,
> please let me know. I would be glad to help get this working as soon as
> possible!
> Thanks,
> Paul

New description:

 HI, I am a geneticist and would love to have "Stacks" ported properly to
 run on Mac OSX. This software enables filtering and alignment of DNA
 sequencing data from next-generation DNA sequencing. It is highly needed!!

 The performance of Stacks can be improved by installing two external
 libraries. Samtools & Google’s SparseHash. These optional packages must be
 installed and enabled prior to building Stacks. Please make sure that
 these are part of the port (I think these are both part of macports
 already).
 http://samtools.sourceforge.net/
 http://code.google.com/p/sparsehash/

 Also, this software is multi-processor aware and GREATLY benefits from
 OpenMP. If this port could make use of OpenMP that would be fantastic! I
 think to do so would require compiling with GCC. Please include OpenMP
 install variants too!!

 From the website, it looks like the following are also needed:
   - mysql-server php5 apache2
   - php-mdb2 php-mdb2-driver-mysql
   - libdbd-mysql-perl
   - samtools
   - libbam-dev

 The files and info on the project are located at:
 http://creskolab.uoregon.edu/stacks/

 I have attached the latest download. If you need any help testing this,
 please let me know. I would be glad to help get this working as soon as
 possible!
 Thanks,
 Paul

--

Comment:

 In the future, please use WikiFormatting. As reporter, you do not need to
 Cc yourself.

-- 
Ticket URL: <https://trac.macports.org/ticket/43300#comment:2>
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