Opened 11 years ago
Last modified 11 years ago
#43300 new request
New port request, Stacks, for Next-Gen DNA short-read sequences
| Reported by: | pst@… | Owned by: | macports-tickets@… |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | |
| Keywords: | Cc: | ||
| Port: | stacks |
Description (last modified by mf2k (Frank Schima))
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
Attachments (1)
Change History (3)
Changed 11 years ago by pst@…
| Attachment: | stacks-1.18.tar.gz added |
|---|
comment:2 Changed 11 years ago by mf2k (Frank Schima)
| Cc: | pst@… removed |
|---|---|
| Description: | modified (diff) |
| Keywords: | NGS Next Generation Sequencing DNA removed |
| Port: | stacks added; Stacks removed |
| Type: | submission → request |
| Version: | 2.2.1 |
In the future, please use WikiFormatting. As reporter, you do not need to Cc yourself.
Latest version as of April, 9, 2014