28df0c35c1
correction of the IR detection
2025-05-25 19:38:01 +02:00
17908e0df2
Patch RPS12 detection
2025-05-25 13:41:47 +02:00
9205fd1ed1
Patch RPS12 detection
2025-05-25 10:31:30 +02:00
c5b92799b1
Detect number of cores
2025-05-24 08:46:13 +02:00
4b71fe8c4c
Changes to be committed:
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modified: .gitignore
new file: data/cds/sp_chlorodb/parameters.sh
deleted: data/ir/LSC_RefDB.fasta
deleted: data/ir/SSC_RefDB.fasta
modified: detectors/cds/bin/go_cds.sh
modified: detectors/normalize/lib/lookforIR.lib.sh
modified: detectors/normalize/lib/selectIR.py
modified: organnot/Dockerfile
new file: organnot/README.md
new file: organnot/dorgannot
deleted: ports/.DS_Store
deleted: src/ncbiblast/binaries/.gitignore
deleted: src/prokov/lxpack/tests/S.fasta
deleted: src/prokov/lxpack/tests/St.fasta
deleted: src/prokov/lxpack/tests/Stt.fasta
deleted: src/prokov/lxpack/tests/aS.fasta
deleted: src/prokov/lxpack/tests/aSt.fasta
deleted: src/prokov/lxpack/tests/aStt.fasta
deleted: src/prokov/lxpack/tests/aaS.fasta
deleted: src/prokov/lxpack/tests/aaSt.fasta
deleted: src/prokov/lxpack/tests/aaStt.fasta
new file: src/repseek/repseek-2014.09.tgz
2025-03-05 21:56:39 +01:00
9d93a68b3a
Change setup for the blast filtering before exonerate
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Former-commit-id: 139685eca58c1fb2272854dee31de3821c54af80
Former-commit-id: dc5c345ce72e9895cbdcc3321499b869040a24da
2022-02-17 18:41:27 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f
Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
2022-02-16 22:50:17 +01:00
e4627ced6e
Switch the go_cds script from tcsh to bash
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Former-commit-id: 36041f96b5bb1411a4ac6fecccfbc24b9b90baff
Former-commit-id: 6e63fdff4022a2bb895a44eb6009f41d049ba4ae
2021-11-04 13:36:28 +01:00
d4da1d01fd
A new set of protein cleaned for the CDS detector prepared using the
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clusterizecore.sh script from the detectors/cds/lib folder.
The CDS detector is now modified to use the clean.fst files.
Former-commit-id: e30a53b5b6b658388af4b2640b30e6765c729894
Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d
2016-10-05 09:31:24 -03:00
536a451510
call explicitely tcsh to workaround a path bug
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Former-commit-id: e6c05a695a6872dd5fb8acd96ee031844dd21fa0
Former-commit-id: 7740135e0861b796e85fce0c9c62a4793f836c2b
2016-04-13 17:32:10 +02:00
f466f5505a
Change tha dash bang of the csh shell scripts
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Former-commit-id: 115a1955c5883ffd0909cb05e887f70fa561b6e6
Former-commit-id: 5e6be182d5a3ec910f5deed27014227f34bd4745
2016-04-13 16:51:58 +02:00
69434c5b86
Add the latest tcsh able to deal with large PATH (at least 4096)
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Former-commit-id: 32011d9b239e2c5ed93646a8173b285f377693a3
Former-commit-id: 6e804387bfacfc4e9242ef3f7014642044f3aa2c
2016-04-13 16:21:50 +02:00
405631f527
cds go_test bug fixed
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Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae
Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
2015-11-13 22:37:22 +01:00
e4d6a8484d
cds/tools/chlorodb added
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Former-commit-id: 0579e878a69b7c285ca71870e9ca5730649a2fda
Former-commit-id: 7cced5b488441d87bf070a9a444317db0e048880
2015-11-13 17:41:18 +01:00
c3c2be254f
go_pass1 moved to bin
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Former-commit-id: 6be837df8518c9374c0a9de6ff717add6178d01b
Former-commit-id: b2e3e8200b9e14447b7eeedd70191e10cf4b8a58
2015-11-09 00:58:50 +01:00
8dab2d56b2
CDS detector added
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Former-commit-id: 93fac7a70052d06c2a12bf8af59820c653edd31b
Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076
2015-11-08 14:28:05 +01:00
