EMBASSY is a collection of contributed EMBOSS software. From the web
pages:
"EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL).
Programs which have been included from third parties who have their own
licencing terms are kept apart under the EMBASSY grouping.
This allows the EMBOSS libraries to link to other software, and only
requires that software to have an LGPL-compatible licence. Phylip, for
example, fits this model.
But, to the user they do look exactly like EMBOSS aplications."
WWW: http://emboss.sourceforge.net/apps/#Embassy
===> The following configuration options are available for embassy-6.2.0_2:
CBSTOOLS=on: CBS Tools
DOMAINATRIX=on: Protein domain apps
DOMALIGN=on: Protein domain apps
DOMSEARCH=on: Protein domain apps
EMNU=on: EMBOSS simple menu
ESIM4=on: Align cDNA/EST to genome
HMMER=on: HMM alignment and searches
IPRSCAN=on: InterPro scan
MEMENEW=on: Motif detection
MIRA=on: Whole Genome shotgun and EST assembler
MSE=on: A multiple sequence screen editor
MYEMBOSS=on: Examples for developers of EMBOSS apps
PHYLIPNEW=on: Phylogeny inference
SIGNATURE=on: Protein domain apps
STRUCTURE=on: Protein domain apps
TOPO=on: Transmembrane display
VIENNA=on: RNA folding
===> Use 'make config' to modify these settings
biology/embassy: specify post-extraction with ${TAR}
It's possible that EXTRACT_CMD won't be predefined in the near future
in order to support distfiles in multiple formats. We know the post-
extraction tool needs to be tar, so let's specify it directly.
This port needs staging. It doesn't like like a quick job so I'm leaving
that to the listed maintainer.
Approved by: infrastructure improvements blanket
Approved by: portmgr (implicit) (to skip stage check)
- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead
PR: 157936
Submitted by: myself
Exp-runs by: pav
Approved by: pav
For EMBOSS:
This patch brings EMBOSS up to date with the current version.
i. The patches included in files/ are bugfixes for files in
EMBOSS-3.0.0 that appeared after the release. They are
documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README
This is just 'for the record' so that we remember to remove these
patches in the next update.
ii. EMBOSS is now installed by default in LOCALBASE/emboss
This is to avoid CONFLICTS with other ports that install files
with the same names. Installing EMBOSS to another PREFIX is also
possible.
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