CCseqBasic5 code changes log file
This log was Last updated by Jelena :
Mon Oct 8 16:56:53 BST 2018
commit 95c29c3ebed098d9fbbb77043544e395a992d844
Author: telenius
Date: Tue Aug 28 16:37:05 2018 +0100
adding intra-house support for some custom genomes
commit f1de6e8641d1a52350d6958784eb2b4d0c3a2348
Author: telenius
Date: Fri Jul 6 15:17:05 2018 +0100
fix to earlier fix
commit adf9a750f8d199c77afc10533a6ed19aa5957ca1
Author: telenius
Date: Fri Jul 6 12:00:08 2018 +0100
fix to the trimming glitch
finally a fix to the leaking trimming quality control - if trimgalore crashes, run will crash too (not continue with untrimmed files as before)
commit 253829172569468ed4652b7bc953b88db2c82904
Author: telenius
Date: Tue Jun 19 10:39:56 2018 +0100
fixing name of generated RE cut genome file
commit 132af36e8bfd624f4d8aa4b5c48d4ecbc1ac003d
Author: telenius
Date: Wed May 30 12:07:48 2018 +0100
fix to yesterdays fix
commit 29d8e2645ebdf3497281b8675d0256daa4ff8b46
Author: telenius
Date: Tue May 29 17:12:56 2018 +0100
fixing bowtie1 -v flag
commit 095284f37e58c5e690d19eca62c587172cb26421
Author: telenius
Date: Fri May 11 16:08:33 2018 +0100
hindIII genome cutter fix
commit 8f182de31f70d1e4031f3ef9030ccc3c37091eaa
Author: telenius
Date: Fri May 4 20:06:36 2018 +0100
fix multitile counters and bowtie -v flag
commit edaa0d88f695d01ff3358d328de48d88eb7f37a7
Author: telenius
Date: Thu May 3 17:20:07 2018 +0100
fixing the counters of 11e and 11ee summary reports - for the flashed files
commit d29910b68494104bbcca477b058190810c51d9ba
Author: Jelena Telenius
Date: Thu May 3 15:48:31 2018 +0100
fixing the counters of 11e and 11ee summary reports
commit ba141958435d93a683c9f45da49f9a9ab1b95ba2
Author: Jelena Telenius
Date: Wed May 2 22:58:38 2018 +0100
fully functional rainbow runs for --tiled and --stopAfterBamCombining
commit 682bfa22634ff16e6964de387dc19ea11c79ef52
Author: Jelena Telenius
Date: Tue May 1 19:45:00 2018 +0100
Functional output html files for fastq-analysis part of rainbow pipe, --tiled flag
commit f9711cda85fd565e153520143b1ebfdee0e97f1d
Author: Jelena Telenius
Date: Fri Apr 27 16:26:46 2018 +0100
misc rainbow pipe small fixes in hindIII and fastq-wise visualisations
commit 4cd767f8b29178224dc54018de51fad413a7f249
Author: Jelena Telenius
Date: Thu Apr 26 16:50:34 2018 +0100
fastq-wise html page, perl fragment counters for oligoBunchWise sam generation
commit 0b857ac2a267ca83fd9e40ab9433509e88152bf6
Author: Jelena Telenius
Date: Wed Apr 25 14:53:55 2018 +0100
hindIII cutter support, nlaIII and dpnII cutter finessing
commit 6768df1b5087a0493e5d8f540af7cb6eb13c12cb
Author: Jelena Telenius
Date: Tue Apr 24 18:15:54 2018 +0100
hindIII cutter debugging
and some first ideas how to get fastq-wise html reports
commit d21086da17a0057b8371c2fdf4c73ae82031331c
Author: Jelena Telenius
Date: Mon Apr 23 15:40:40 2018 +0100
working summary figure in parallel folder B
commit 4a8f5123fcd58eb0d10628d9f9cc8f0f2f982761
Author: Jelena Telenius
Date: Mon Apr 23 14:47:33 2018 +0100
generating parallel figures - more additions
commit 4a1f5ecd1d91c09c862691a14fb44ef665080862
Author: Jelena Telenius
Date: Sun Apr 22 15:39:01 2018 +0100
first tries to get hindIII support working
commit 80f687108e0fce539e93101e3d9a6711092675fe
Author: Jelena Telenius
Date: Sun Apr 22 11:35:01 2018 +0100
updating the new paths to the figure generation scripts
plus starting to build separate figure generator script for combined
fastq counts in rainbow run
commit d6e8d87896b596741aab2a9bf5fa4c6c54754af8
Author: Jelena Telenius
Date: Sun Apr 22 11:25:41 2018 +0100
moving scripts around (NOTE THIS IS COMMIT GENERATES A BROKEN RELEASE)
Putting figure-generating scripts to "common subroutines" (as both
serial and parallel codes use those). This is just MOVING the scripts to
the new location, so running a pipe generated from this commit will not
work.
The commit just after this will be updating the new locations of the
scripts to the codes,
thus generating runnable version
commit f3bb834ab881703d764e8b419e55498426bc55ea
Author: Jelena Telenius
Date: Thu Apr 19 18:21:01 2018 +0100
fixing counters in bam file loops
commit 4f41009da995479b0fb50921a0219e84836763ba
Author: Jelena Telenius
Date: Thu Apr 19 16:55:19 2018 +0100
fixing bam combining sub for rainbow pipe
commit ba22d19ec7b613338989212835946e872428448b
Author: Jelena Telenius
Date: Thu Apr 19 14:40:55 2018 +0100
misc parallelisation edits - to sync dev and production pipes
commit 114b9b15ae89dc871abb86fe1eb0000228490bd1
Author: Jelena Telenius
Date: Wed Apr 18 18:07:29 2018 +0100
oligo loop break - for large oligo counts
commit 14995b9aa189217f0172d3dd00eb227d2ee626d0
Author: Jelena Telenius
Date: Fri Apr 13 15:50:13 2018 +0100
adding flag --stopAfterBamCombining to allow runs with the not-yet-so-functional pipe
commit 075d25c5d2839c61f81002e72a8e09d8ae9a31df
Author: Jelena Telenius
Date: Wed Apr 11 17:00:06 2018 +0100
matplotlib version test
matplotlib version test and preliminary finetuning of other codes, to
get blat parts working
commit 05abe27c5314bd2e717d9d94d3b84915a0c540ed
Author: Jelena Telenius
Date: Thu Mar 22 17:03:12 2018 +0000
pre-parallel changes 8 - first tries to get blat working
building the loop structures and error log structure for blat and
"parallel part 2" and "oligo" loops.
commit e1702b649064add8bdadfddae7f470dd68ad98a3
Author: Jelena Telenius
Date: Thu Mar 22 10:55:30 2018 +0000
allowing lowercase_v to be empty in parameter setting
commit 7be7bba62d094cea9cfb5b77200fd97b6b363214
Author: Jelena Telenius
Date: Thu Mar 22 10:48:25 2018 +0000
typo fix in cd tester
commit 9054a2137dba0a76f0e3051f38011c7372e0ba88
Author: Jelena Telenius
Date: Wed Mar 21 18:21:24 2018 +0000
adding "weird character tester" to rm mv cd testers
commit 3c7b022f8852820d81e38ae7ce2cb9bfbf658e3e
Author: Jelena Telenius
Date: Wed Mar 21 17:03:04 2018 +0000
adding * and .. to forbidden parts of mv rm and cd commands
commit ac5916e2c7f86fab0c09250ef58cdb99d0e29d1c
Author: Jelena Telenius
Date: Tue Mar 20 18:48:44 2018 +0000
pre-parallel mods 7
CCseqBasic5.sh works as before.
CCseqBasic5_rainbow.sh has working OLIGObunches folder generation, as
well as working folder C/F1 folder generation. Folders C/F2 and C/F3
start but hub fails. Blat not yet tested.
commit fe57a1e12772e3dc5b5561b1e740dc2d5c8647ca
Author: Jelena Telenius
Date: Tue Mar 20 16:37:56 2018 +0000
re-organising the scripts final touches 2
commit d5099d597710c96dc8b48ac059bc5d958bfcf0a3
Author: Jelena Telenius
Date: Tue Mar 20 15:52:00 2018 +0000
re-organising the scripts final touches
commit 144a9b68e260cc8df4bc229375fd114f881de747
Author: Jelena Telenius
Date: Mon Mar 19 19:37:08 2018 +0000
re-organising script folders to "parallel" and "serial"
commit e703b45fccab653809bf7a789c2a64ef3f15d2c8
Author: Jelena Telenius
Date: Mon Mar 19 19:00:42 2018 +0000
pre-parallel mods testing - small typo fixes
commit a7d6d617cf39f842c7f52a6befacddc766c36778
Author: Jelena Telenius
Date: Mon Mar 19 16:44:09 2018 +0000
final touchers tester-of-tester cd mv rm commands
commit fb08855e1aafdf09fc7183edfc5ef52d47c73c5e
Author: Jelena Telenius
Date: Mon Mar 19 16:31:24 2018 +0000
finishing touches for the rm cd mv tester : tester script for testers
commit 226a28ce2720db012653e3e1203551d59dfed699
Author: Jelena Telenius
Date: Sun Mar 18 18:16:51 2018 +0000
finishing touches for the rm mv cd safety features (rainbow script support)
commit f701bf446eef88ddb788af4ae0ffff5e2cb7329a
Author: Jelena Telenius
Date: Sun Mar 18 17:31:24 2018 +0000
safety subroutines for mv cd and rm commands
commit 43ee4f9eeea724736c62229a7d471a994aa05ef8
Author: Jelena Telenius
Date: Thu Mar 15 17:02:16 2018 +0000
pre-parallel mods 6 , adding debugging options (commented out), separate fastqc and bowtie log reports
commit 29ecba28c0a9e0e3564ea4dc33fe51b0040d21b3
Author: Jelena Telenius
Date: Mon Mar 12 19:38:57 2018 +0000
pre-parallel mods 5
CCseqBasic5.sh works as before. CCseqBasic5_rainbow.sh runs now with
--stopAfterFolderB without errors. Folders C and D are still broken.
MultiQC reports are generated properly in folder B.
commit dfb0398520df8e2c041dbf9bf63d01610ad54dc9
Author: Jelena Telenius
Date: Mon Mar 12 16:11:04 2018 +0000
flag --useSymbolicLinks final touches
commit 32b54056e489f4891806b0bc99ea518eecd0a773
Author: Jelena Telenius
Date: Mon Mar 12 14:35:36 2018 +0000
functional --useSymbolicLinks flag
commit db72953f5aefc7f6bb976b8de9bef6a7f38c0995
Author: Jelena Telenius
Date: Fri Mar 9 17:02:27 2018 +0000
vanishing FLASHED tracks fix, first (not working) try for flag --useSymbolicLinks
commit 2cef4c2c1b5c97e61a4f7d6b31e21cef0d032506
Author: Jelena Telenius
Date: Fri Mar 9 16:26:15 2018 +0000
Update README.md
commit 0c08a12e90e83413f8d7d89d7cb230ed94b39240
Author: Jelena Telenius
Date: Thu Mar 8 19:44:37 2018 +0000
fastqc version upgrade, samtools sort version upgrade
commit 13a74f5d4259bf5a8b3dc0f472394522a7e9f221
Author: Jelena Telenius
Date: Mon Mar 5 19:44:34 2018 +0000
tool version change support fixes
commit 59cfa8a0ed8c8ec3a8999a6c4731877864673e75
Author: Jelena Telenius
Date: Mon Mar 5 18:46:29 2018 +0000
typo correction in output log on-the-fly hub addresses
commit d4c9fe7a6d0de07a174b08ca33820a7254cb4ff2
Author: Jelena Telenius
Date: Mon Mar 5 15:05:39 2018 +0000
figure make fix : flash log parse to support new versions of flash
commit 0168aa0130233e73028fd6e689cfd3dcb19874c4
Author: Jelena Telenius
Date: Mon Mar 5 14:20:17 2018 +0000
Updating testEnvironment to recognise new folder structure
commit 463c157736f3952e497ebecbcb992fcb1c9f1b31
Author: Jelena Telenius
Date: Thu Mar 1 16:10:55 2018 +0000
added a note about ucstools
commit fa3a3903c6991d920466919a3235e87f3a419706
Author: Jelena Telenius
Date: Thu Mar 1 15:12:39 2018 +0000
Update README.md
commit 31075688374e9eb59fab3547fca0eadc5d841a0b
Author: Jelena Telenius
Date: Thu Mar 1 15:12:22 2018 +0000
Update README.md
commit 5fe5b44ac133af528830d4c0c100642f7f3b7907
Author: Jelena Telenius
Date: Thu Mar 1 15:11:31 2018 +0000
Update README.md
commit dd78beccb27859c05c6525684ff63c1e4e0b689d
Author: Jelena Telenius
Date: Thu Mar 1 15:11:18 2018 +0000
Update README.md
commit 68774c1d2944726cc0f05974ce1c86c00aea4231
Author: Jelena Telenius
Date: Thu Mar 1 15:10:25 2018 +0000
Update README.md
commit a6d682fd264232f33e329edca804e2bb2763225e
Author: Jelena Telenius
Date: Thu Mar 1 15:09:02 2018 +0000
Update README.md
commit d66cd8b9e57c8df6446a61251c1a611ab90612bf
Author: Jelena Telenius
Date: Thu Mar 1 15:08:50 2018 +0000
Update README.md
commit 5a8e3b3b14da73dd98ac62f56934a555748fc5ae
Author: Jelena Telenius
Date: Thu Mar 1 15:08:26 2018 +0000
Update README.md
commit e42aec8f53b71a947a4f13e268c43544adb16a34
Author: Jelena Telenius
Date: Thu Mar 1 15:07:53 2018 +0000
Update README.md
commit 3da3a82d03a8cf3c5ba2ec92b84a8154bb0544e1
Author: Jelena Telenius
Date: Thu Mar 1 15:07:01 2018 +0000
Update README.md
commit ddf684a79ed5fab74766a083ae415fc4fd6e1202
Author: Jelena Telenius
Date: Mon Feb 26 14:59:09 2018 +0000
remove a script file which wasn't needed
commit a22b5d4feae796a75d261ee9deeb883dc345cc7f
Author: Jelena Telenius
Date: Mon Feb 26 13:47:11 2018 +0000
Disabling the makeSymbolicLinks subroutine : no symlinks in public from now on
commit 3a931d9d9b8374ab114ad25e369db95408155c20
Author: Jelena Telenius
Date: Fri Feb 23 18:26:42 2018 +0000
pre-parallel changes 4 , --onlyBlat flag addition
Main script CCanslyser5.sh works as before. New flag --onlyBlat should
work now (you still have to give parameters -o --R1 and --R2 and these
files have to exist but the script doesn't use the them for anything).
CCanalyser_serial.sh works for folders A_prepareForRun
B_mapAndDivideFastqs , but not further than that (this is approximately
the old folder F1 , plus dividing bams to oligo-file bunches).
commit 4b6335ae2552c7e592d321953f84773815deb6e3
Author: Jelena Telenius
Date: Thu Feb 22 13:40:51 2018 +0000
re-organising the code folders + third code changes preparing for parallelisation
CCanalyser5.sh is still the main script, but on the side of it building
a sister script CCanalyser5_serial.sh which will be the "new way" to run
the pipe (and serves as the serial excecution sister of the new parallel
pipe). CCanalyser5_serial.sh doesn't work yet.
commit abbed6530a9c236a8a56d3410bf1cd9581880141
Author: Jelena Telenius
Date: Mon Feb 19 17:00:02 2018 +0000
parallel support : COMBINED bigwigs hub
commit 39a6481bba64e4bde8f253cb1b6d7c09cb03124f
Author: Jelena Telenius
Date: Mon Feb 19 15:53:56 2018 +0000
preparing for parallelisation 2
normal runs work as before.
Parallelisation tested and working for --onlyREdigests and --parallel 1
, also when combined to --onlyCCanalyser .Runs through in --parallel 2
, but COMBINED bigwigs hub breaks as color numbering is not bug-free
yet.
commit 9aadfbc61e8016ec696c00ecc4b66fb84be249fd
Author: Jelena Telenius
Date: Mon Feb 19 11:04:22 2018 +0000
genomes.txt file portability bug fix
commit 2abe8dad7fbbfabae30b8b984517fb33944b6301
Author: Jelena Telenius
Date: Thu Feb 15 13:52:55 2018 +0000
building support for the coming parallelisation
Adding the special run mode of F1 and F2 "only-divide-bams" , along with
the oligo bunch parameter. Creating mainRunner.sh and defaultparams.sh
to make main script CCseqBasic5.sh more readable, and subroutines more
importable for the coming parallelisation script, when the
parallelisation will be rolled in.
commit c5021fd2c9dd14fc7002508df9f05aab689565a3
Author: Jelena Telenius
Date: Thu Jan 25 18:13:20 2018 +0000
fp command bug fix
commit 5322e1482750a362286522fdc549d73b14252eeb
Author: Jelena Telenius
Date: Tue Jan 16 18:08:47 2018 +0000
reporting filtered TRANS fragments in ccanalyser.pl
commit d6593a5c9e5063af012729ad15abc1ad5e30a2ef
Author: Jelena Telenius
Date: Tue Jan 16 17:43:39 2018 +0000
Adding --onlyCis and --sonicationSize 300 flags to speed up runs
--onlyCis : only cis reads are analysed. this also generates blat-files
for only cis chromosome
--sonicationSize 300 : how many bases max fragment lenght. stuff farther
away from cut site than this, is considered invalid and filtered in the
end of folder F1
commit c0c13858e3bf4a1844e10b24437c7531b6f44568
Author: Jelena Telenius
Date: Mon Jan 8 14:55:20 2018 +0000
still one more fp : fix for portability
commit 5509ba7ac2f545b1a78b70da3e1ddb908ce9bc53
Author: Jelena Telenius
Date: Wed Jan 3 18:22:06 2018 +0000
typo correction in the oligo file portability fix
commit e5e33894069b04e0b9c734f8c41004d365592dbb
Author: Jelena Telenius
Date: Fri Dec 29 14:36:10 2017 +0000
fp command out for portability, tester script mod for new location of ucsctools scripts
commit f40870096cf111211ff119068d5de2d8cf2e97fb
Author: Jelena Telenius
Date: Tue Dec 19 15:25:14 2017 +0000
ucsctools and blat less conflict prone
commit 0ec5fdc177a5486bbdd5af8ecbf532f8f293a8fb
Author: Jelena Telenius
Date: Tue Dec 19 14:19:24 2017 +0000
path export better, ucsctools and blat less conflict prone
path export had poor examples of needed paths to be exported. ucsctools
may contain same name script names as blat, thus exporting ucsctools
from the conf/ucsctools instead
commit 75253f7e2cb358a465f4da1039620c983e75ed0c
Author: Jelena Telenius
Date: Wed Dec 13 13:03:47 2017 +0000
deleting outdated comments about adding new genomes
commit 1f4b09995d595630e04f8f53be3b628b7bd782f4
Author: Jelena Telenius
Date: Mon Nov 20 11:32:42 2017 +0000
bowtie 2 support, name change to CB5
commit 72f68000871bb4a9079fbdeea0327f7d538a3120
Author: Jelena Telenius
Date: Mon Nov 20 10:09:35 2017 +0000
Starting point : CS5 as it was 20Nov2017
commit 25e6b366b64109950a501e83fd41162e9e5ad9d7
Author: Jelena Telenius
Date: Mon Nov 20 10:07:32 2017 +0000
Update README.md
commit 9be0c132677a0b53136a7226565245a115ed3192
Author: Jelena Telenius
Date: Mon Nov 20 10:06:57 2017 +0000
Initial commit