BSD Ports

biology/fastqc 0.12.1_2 FreeBSD

Quality control tool for high throughput sequence data

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
GPLv3
Categories
biology, java, perl5
Package size
10992.2 KiB, 12164.8 KiB installed

Description

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

In the other systems

SystemPortVersion
FreeBSDbiology/fastqc0.12.1_2
NetBSDbiology/fastqc0.11.9nb2
DragonFlybiology/fastqc0.12.1
HardenedBSDbiology/fastqc0.12.1_2
GhostBSDbiology/fastqc0.12.1_2

Install

Binary package:

pkg install fastqc

From the ports tree:

cd /usr/ports/biology/fastqc/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	fastqc>0:biology/fastqc

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.12.1_20.12.1_20.11.90.12.10.12.1_2
FreeBSD:14:quarterly0.12.1_20.12.1_2n/a0.12.10.12.1_2
FreeBSD:15:latest0.12.1_20.12.1_2n/a0.12.10.12.1
FreeBSD:15:quarterly0.12.1_20.12.1_2n/an/an/a
FreeBSD:16:latest0.12.1_20.12.1_2n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Run dependencies 54

Configuration

No options to configure.

USES
java zip perl5 shebangfix
Service scripts
none

Message after installing

===>   NOTICE:

The fastqc port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 248
  • bin/fastqc
  • share/fastqc/Configuration/adapter_list.txt
  • share/fastqc/Configuration/contaminant_list.txt
  • share/fastqc/Configuration/limits.txt
  • share/fastqc/Help/1 Introduction/.svn/entries
  • share/fastqc/Help/1 Introduction/.svn/text-base/1.1 What is FastQC.html.svn-base
  • share/fastqc/Help/1 Introduction/1.1 What is FastQC.html
  • share/fastqc/Help/2 Basic Operations/.svn/entries
  • share/fastqc/Help/2 Basic Operations/.svn/text-base/2.1 Opening a sequence file.html.svn-base
  • share/fastqc/Help/2 Basic Operations/.svn/text-base/2.2 Evaluating Results.html.svn-base
  • share/fastqc/Help/2 Basic Operations/.svn/text-base/2.3 Saving a Report.html.svn-base
  • share/fastqc/Help/2 Basic Operations/2.1 Opening a sequence file.html
  • share/fastqc/Help/2 Basic Operations/2.2 Evaluating Results.html
  • share/fastqc/Help/2 Basic Operations/2.3 Saving a Report.html
  • share/fastqc/Help/3 Analysis Modules/.svn/entries
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/duplication_levels.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/kmer_profiles.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_gc_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_n_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_sequence_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_gc_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_tile_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/prop-base/sequence_length_distribution.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/1 Basic Statistics.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/10 Adapter Content.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/11 Kmer Content.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/12 Per Tile Sequence Quality.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/2 Per Base Sequence Quality.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/3 Per Sequence Quality Scores.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/4 Per Base Sequence Content.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/5 Per Sequence GC Content.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/6 Per Base N Content.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/7 Sequence Length Distribution.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/8 Duplicate Sequences.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/9 Overrepresented Sequences.html.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/duplication_levels.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/kmer_profiles.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_gc_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_n_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_sequence_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_gc_content.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/per_tile_quality.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/.svn/text-base/sequence_length_distribution.png.svn-base
  • share/fastqc/Help/3 Analysis Modules/1 Basic Statistics.html
  • share/fastqc/Help/3 Analysis Modules/10 Adapter Content.html
  • share/fastqc/Help/3 Analysis Modules/11 Kmer Content.html
  • share/fastqc/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html
  • share/fastqc/Help/3 Analysis Modules/2 Per Base Sequence Quality.html
  • share/fastqc/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html
  • share/fastqc/Help/3 Analysis Modules/4 Per Base Sequence Content.html
  • share/fastqc/Help/3 Analysis Modules/5 Per Sequence GC Content.html
  • share/fastqc/Help/3 Analysis Modules/6 Per Base N Content.html
  • share/fastqc/Help/3 Analysis Modules/7 Sequence Length Distribution.html
  • share/fastqc/Help/3 Analysis Modules/8 Duplicate Sequences.html
  • share/fastqc/Help/3 Analysis Modules/9 Overrepresented Sequences.html
  • share/fastqc/Help/3 Analysis Modules/duplication_levels.png
  • share/fastqc/Help/3 Analysis Modules/kmer_profiles.png
  • share/fastqc/Help/3 Analysis Modules/per_base_gc_content.png
  • share/fastqc/Help/3 Analysis Modules/per_base_n_content.png
  • share/fastqc/Help/3 Analysis Modules/per_base_quality.png
  • share/fastqc/Help/3 Analysis Modules/per_base_sequence_content.png
  • share/fastqc/Help/3 Analysis Modules/per_sequence_gc_content.png
  • share/fastqc/Help/3 Analysis Modules/per_sequence_quality.png
  • share/fastqc/Help/3 Analysis Modules/per_tile_quality.png
  • share/fastqc/Help/3 Analysis Modules/sequence_length_distribution.png
  • share/fastqc/Templates/Icons/error.png
  • share/fastqc/Templates/Icons/fastqc_icon.png
  • share/fastqc/Templates/Icons/tick.png
  • share/fastqc/Templates/Icons/warning.png
  • share/fastqc/Templates/fastqc2fo.xsl
  • share/fastqc/Templates/header_template.html
  • %%JAVAJARDIR%%/fastqc/cisd-jhdf5.jar
  • %%JAVAJARDIR%%/fastqc/htsjdk.jar
  • %%JAVAJARDIR%%/fastqc/jbzip2-0.9.jar
  • %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$1.class
  • %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$InputStream.class
  • %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$OutputStream.class
  • %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/AllowedSolution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BrentSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolver.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolverUtils.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractIntegerDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution$1.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/BetaDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/BinomialDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/CauchyDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/ChiSquaredDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/FDistribution.class
  • %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/GammaDistribution.class

The first 100 are listed.

distinfo 1
FileSizeSHA256
fastqc_v0.12.1.zip1.1709692e+075f4dba8780231a25a6b8e11ab2c238601920c9704caa5458d9de559575d58aa7
Master sites 1
  • https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon 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.