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Port details
ddocent Bash pipeline for RAD sequencing
2.2.25 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: 20 Apr 2018 01:34:22
Also Listed In: java
License: MIT
dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost
any kind of RAD sequencing. If you have a reference already, dDocent can be
used to call SNPs from almost any type of NGS data set. It is designed to run
on Linux based machines with large memory capacity and multiple processing
cores, and it can be modified for use on HPC.

WWW: http://ddocent.com
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (20 items)
  1. /usr/local/share/licenses/dDocent-2.2.25/catalog.mk
  2. /usr/local/share/licenses/dDocent-2.2.25/LICENSE
  3. /usr/local/share/licenses/dDocent-2.2.25/MIT
  4. bin/ErrorCount.sh
  5. bin/RefMapOpt.sh
  6. bin/ReferenceOpt.hyb.sh
  7. bin/ReferenceOpt.sh
  8. bin/Rename_SequenceFiles.sh
  9. bin/Rename_for_dDocent.sh
  10. bin/Rename_for_dDocent_with-INDEX.sh
  11. bin/dDocent
  12. bin/dDocent_filters
  13. bin/dDocent_ngs.sh
  14. bin/ddocent-assembly-test
  15. bin/ddocent-assembly-test-cleanup
  16. bin/filter_hwe_by_pop.pl
  17. bin/filter_missing_ind.sh
  18. bin/pop_missing_filter.sh
  19. bin/remake_reference.sh
  20. bin/remove.bad.hap.loci.sh
  21. Collapse this list.

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

PKGNAME: dDocent

distinfo:

TIMESTAMP = 1520345850
SHA256 (jpuritz-dDocent-v2.2.25_GH0.tar.gz) = 903c3010b29b2ca95f7fe6099925948e4d3f21655668caff653df97dfa7ecf44
SIZE (jpuritz-dDocent-v2.2.25_GH0.tar.gz) = 336804


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

Build dependencies:
  1. python2.7 : lang/python27
  2. perl5>=5.26<5.27 : lang/perl5.26
Runtime dependencies:
  1. unzip>=0 : archivers/unzip
  2. mawk>=0 : lang/mawk
  3. gawk>=0 : lang/gawk
  4. coreutils>=0 : sysutils/coreutils
  5. gnuplot>=0 : math/gnuplot
  6. parallel>=0 : sysutils/parallel
  7. bash : shells/bash
  8. bwa>=0.7.13 : biology/bwa
  9. cd-hit>=0 : biology/cd-hit
  10. samtools>=1.3 : biology/samtools
  11. vcftools>=0.1.15 : biology/vcftools
  12. trimmomatic>=0 : biology/trimmomatic
  13. bamtools>=0 : biology/bamtools
  14. stacks>=0 : biology/stacks
  15. rainbow>=0 : biology/rainbow
  16. trimadap>=0 : biology/trimadap
  17. seqtk>=0 : biology/seqtk
  18. bedtools>=2.26.0 : biology/bedtools
  19. pear-merger>=0 : biology/pear-merger
  20. vcflib>=0 : biology/vcflib
  21. freebayes : biology/freebayes
  22. java : java/openjdk8
  23. python2.7 : lang/python27
  24. perl5>=5.26<5.27 : lang/perl5.26
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
perl5 python shebangfix

Master Sites:
  1. https://codeload.github.com/jpuritz/dDocent/tar.gz/v2.2.25?dummy=/

Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Apr 2018 01:34:05
Original commit files touched by this commit  2.2.25
Revision:467808
jwb search for other commits by this committer
biology/ddocent: Bash pipeline for RAD sequencing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15139

Number of commits found: 1

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