Package list barrnap / fcd722f
split up HMMs to go into free and non-free packages Sascha Steinbiss 6 years ago
5 changed file(s) with 64 addition(s) and 6 deletion(s). Raw diff Collapse all Expand all
0 db/nonfree/euk.hmm usr/share/barrnap/db/nonfree
1 db/nonfree/arc.hmm usr/share/barrnap/db/nonfree
2 db/nonfree/bac.hmm usr/share/barrnap/db/nonfree
00 bin/barrnap usr/bin
1 db usr/share/barrnap
1 db/free/euk.hmm usr/share/barrnap/db
2 db/free/arc.hmm usr/share/barrnap/db
3 db/free/bac.hmm usr/share/barrnap/db
00 Source: barrnap
1 Section: non-free/science
21 Priority: optional
32 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
43 Uploaders: Sascha Steinbiss <sascha@steinbiss.name>
5 Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1)
4 Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1), lua5.1, dh-exec
65 Standards-Version: 3.9.6
76 Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml
87 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/barrnap/trunk/
109
1110 Package: barrnap
1211 Architecture: all
12 Section: science
1313 Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, hmmer (>= 3.1)
1414 Description: rapid ribosomal RNA prediction
1515 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of
2020 NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.
2121 Multithreading is supported and one can expect roughly linear speed-ups
2222 with more CPUs.
23
24 Package: barrnap-silva-hmms
25 Architecture: any
26 Section: non-free/science
27 Depends: barrnap
28 Description: non-free pHMMs for barrnap
29 Profile Hidden Markov models (pHMMs) for use with Barrnap (BAsic Rapid
30 Ribosomal RNA Predictor), which are only free to use for academic users.
0 #!/usr/bin/env lua
1
2 function usage()
3 io.stderr:write(string.format("Usage: %s <filter> [<invert>] < file\n", arg[0]))
4 io.stderr:write('Filters out a HMM with NAME matching <filter>.\n')
5 os.exit(1)
6 end
7
8 if #arg < 1 then
9 usage()
10 end
11
12 lastname = nil
13 lines = {}
14 for l in io.lines() do
15 name = l:match('NAME%s+(.*)')
16 table.insert(lines, l)
17 if name then
18 lastname = name
19 elseif l:match('//') then
20 if arg[2] then
21 if lastname:match(arg[1]) then
22 print(table.concat(lines, '\n'))
23 end
24 else
25 if not lastname:match(arg[1]) then
26 print(table.concat(lines, '\n'))
27 end
28 end
29 lines = {}
30 end
31 end
32
33
34
99 dh $@ --parallel
1010
1111 override_dh_auto_build:
12 mkdir db/free
13 debian/filter_hmms.lua 28S < db/euk.hmm > db/free/euk.hmm
14 debian/filter_hmms.lua 23S < db/arc.hmm > db/free/arc.hmm
15 debian/filter_hmms.lua 23S < db/bac.hmm > db/free/bac.hmm
16 mkdir db/nonfree
17 debian/filter_hmms.lua 28S t < db/euk.hmm > db/nonfree/euk.hmm
18 debian/filter_hmms.lua 23S t < db/arc.hmm > db/nonfree/arc.hmm
19 debian/filter_hmms.lua 23S t < db/bac.hmm > db/nonfree/bac.hmm
20
21 override_dh_auto_install:
1222 # pass
1323
14 override_dh_auto_install:
15 # pass
24 override_dh_auto_clean:
25 rm -rf db/free db/nonfree
1626
1727 get-orig-source:
1828 uscan --verbose --force-download --repack --compression xz --destdir=..
19 mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz
29 mv ../barrnap_$(OVERSION).orig.tar.xz ../barrnap_$(VERSION).orig.tar.xz
2030