Port details
rna-seq Metaport for RNA-Seq analysis
0.2.0 biology Σ 0.2.0Version of this port present on the latest quarterly branch. There is no maintainer for this port. Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org Port Added: 2022-12-14 00:00:51Last Update: 2026-10-08 13:42:17Commit Hash: 2414383 Also Listed In: python License: NAWWW: https://github.com/auerlab/ Description: # Metaport to install tools for typical RNA-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis. Manual pages: # FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist # USE_RC_SUBR (Service Scripts)
no SUBR information found for this port
Dependency lines :
rna-seq>0:biology/rna-seq To install the port : # cd /usr/ports/biology/rna-seq/ && make install clean To add the package , run one of these commands: pkg install biology/rna-seq pkg install rna-seq PKGNAME: rna-seq Flavors: there is no flavor information for this port. # distinfo: # TIMESTAMP = 1772667504
Packages (timestamps in pop-ups are UTC): #
Dependencies # NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered. Build dependencies: #
python3.12 : lang/python312
Test dependencies: #
python3.12 : lang/python312
Runtime dependencies: #
sra-tools>0 : biology/sra-tools fastq-trim>0 : biology/fastq-trim fastqc>0 : biology/fastqc py312-multiqc>0 : biology/py-multiqc@py312 biolibc-tools>0 : biology/biolibc-tools gffread>0 : biology/gffread kallisto>0 : biology/kallisto hisat2>0 : biology/hisat2 rna-STAR>0 : biology/star samtools>0 : biology/samtools fasda>0 : biology/fasda fasda-utils>0 : biology/fasda-utils webbrowser>0 : www/webbrowser curl>0 : ftp/curl python3.12 : lang/python312
There are no ports dependent upon this port # Configuration Options : # No options to configure Options name : # biology_rna-seq USES: # metaport python
FreshPorts was unable to extract/find any pkg message # Master Sites: # There is no master site for this port.
Number of commits found: 9 #
Commit History - (may be incomplete: for full details, see links to repositories near top of page) Commit Credits Log message 0.2.0 Jason W. Bacon (jwb) Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream. 0.2.0 Jason W. Bacon (jwb) biology/rna-seq: Update to 0.2.0
Add biology/fasda-utils to metaport depends 0.1.4_1 Rene Ladan (rene) all: bump PORTREVISION after updating graphics/libyuv
Using the Tools/scripts/bump_revision.pl script 0.1.4 Jason W. Bacon (jwb) biology/rna-seq: Add biology/star dep to metaport 0.1.3 Jason W. Bacon (jwb) biology/rna-seq: Add curl to metaport deps
Standardizing on a download tool simplifies pipelines 0.1.2_1 Gerald Pfeifer (gerald) *: Bump PORTREVISIONs for math/mpc update to 1.3.1 0.1.2 Jason W. Bacon (jwb) biology/rna-seq: Drop biology/igv dep
Non-essential and currently broken 0.1.1 Jason W. Bacon (jwb) biology/rna-seq: Update to 0.1.1
Fix WWW
Add www/webbrowser for portable FastQC report viewing 0.1.0 Jason W. Bacon (jwb) biology/rna-seq: Metaport for RNA-Seq analysis
Metaport to install tools for typical RNA-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
Number of commits found: 9
