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Port details
kallisto Quantify abundances of transcripts from RNA-Seq data
0.43.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 02 Dec 2017 20:44:35
License: BSD2CLAUSE
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
data, or more generally of target sequences using high-throughput sequencing
reads. It is based on the novel idea of pseudoalignment for rapidly determining
the compatibility of reads with targets, without the need for alignment.

WWW: https://pachterlab.github.io/kallisto/about.html
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (5 items)
  1. bin/kallisto
  2. bin/kallisto-test
  3. /usr/local/share/licenses/kallisto-0.43.1/catalog.mk
  4. /usr/local/share/licenses/kallisto-0.43.1/LICENSE
  5. /usr/local/share/licenses/kallisto-0.43.1/BSD2CLAUSE
  6. Collapse this list.

To install the port: cd /usr/ports/biology/kallisto/ && make install clean
To add the package: pkg install kallisto

PKGNAME: kallisto

distinfo:

TIMESTAMP = 1512166931
SHA256 (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e
SIZE (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 1067076


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cmake : devel/cmake
  2. ninja : devel/ninja
Library dependencies:
  1. libhdf5.so : science/hdf5
  2. libsz.so : science/szip
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for kallisto-0.43.1:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
cmake compiler:c++11-lang

Master Sites:
  1. https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.43.1?dummy=/

Number of commits found: 2

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
02 Jun 2018 19:40:59
Original commit files touched by this commit  0.43.1
Revision:471400
linimon search for other commits by this committer
Adjust USES to fix building on gcc-based archs (in particular, powerpc64).

On the clang architectures, these changes have no effect: the baser
compiler already includes the needed features.

While here, remove now-redundant CXXFLAGS statements and pet portlint
(no other content change).

Tested on both powerpc64 and amd64.

Approved by:	portmgr (tier-2 blanket)
02 Dec 2017 20:44:28
Original commit files touched by this commit  0.43.1
Revision:455382
jwb search for other commits by this committer
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328

Number of commits found: 2

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