CCseqBasic3 code changes log file
This log was Last updated by Jelena :
Mon Oct 8 16:56:53 BST 2018
commit 0c48ae522e351a6f3d6af17572a4e674dffbc33f
Author: telenius
Date: Fri Jul 6 15:16:20 2018 +0100
fix to earlier fix
commit 99797c2d48b5f1e2160e90d75f02e8b7e063d4be
Author: telenius
Date: Fri Jul 6 12:20:31 2018 +0100
intra-WIMM public area support
commit 42102f5be47f56d123786c0d1a03c69cd1166249
Author: telenius
Date: Fri Jul 6 11:57:21 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 f752116d917168b98ae10508bebd01e24c7872f2
Author: telenius
Date: Tue Jun 19 10:38:49 2018 +0100
fixing name of generated RE cut genome file
commit fcd3fe75acbb3e9e1114eedf890b790f6a10dd34
Author: telenius
Date: Wed May 30 12:06:12 2018 +0100
fix to yesterdays fix
commit 35464307f89652c2e87cdd9752716c3859cdb396
Author: telenius
Date: Tue May 29 17:08:56 2018 +0100
fixing bowtie1 -v flag
commit c21d1108da6db8a7be4c4ba49ee85b533b4a87c7
Author: telenius
Date: Fri May 11 16:03:06 2018 +0100
removing hindIII - will not support
commit 2fa6ab0b59dc63bbb5ea1ca6e47f84adfe1f7a39
Author: telenius
Date: Fri May 4 20:07:12 2018 +0100
fixing bowtie -v flag
commit 524bac85c0abdcddd7c239e27bbd64b37ddb2e10
Author: Jelena Telenius
Date: Thu Mar 8 19:43:28 2018 +0000
fastqc version upgrade, samtools sort version upgrade
commit 4cdf18220510fe98d34d4595f893380460b614ad
Author: Jelena Telenius
Date: Mon Mar 5 18:45:22 2018 +0000
typo correction in output log on-the-fly hub addresses
commit 6e8f8f792ffeae614768c84e3d470bba236f3e93
Author: Jelena Telenius
Date: Thu Mar 1 16:12:49 2018 +0000
added a note about ucstools
commit f7aea9339465fbe7e85b99bfc2a22d50f573ff12
Author: Jelena Telenius
Date: Thu Mar 1 16:03:29 2018 +0000
Update README.md
commit 29c06fa4eed3e0fa47639cbb72ac4043c18125df
Author: Jelena Telenius
Date: Thu Mar 1 15:41:04 2018 +0000
Update LICENSE
commit 90a28c52d06ed4cbd7a4fcd25daea8062406ce0c
Author: Jelena Telenius
Date: Thu Mar 1 15:40:40 2018 +0000
Update LICENSE
commit 3e1634b3704646f2e16c63d15e87046af0f647c5
Author: Jelena Telenius
Date: Thu Mar 1 15:16:21 2018 +0000
Update README.md
commit ce267d221a95f5e28ebea4f6f3ea79da5cbbb633
Author: Jelena Telenius
Date: Mon Feb 26 13:46:06 2018 +0000
Disabling the makeSymbolicLinks subroutine : no symlinks in public from now on
commit 51e035a14ec9818c79116892765e86ddcd59d6e1
Author: Jelena Telenius
Date: Mon Feb 19 11:03:44 2018 +0000
genomes.txt file portability bug fix
commit d53d3f69e93e06ba693a2f6ab1b5534be65e43fa
Author: Jelena Telenius
Date: Wed Jan 3 18:21:12 2018 +0000
typo correction in the portable oligo files fix
commit c3bca30947f5056a9c8b5d246228e086a6a3dc29
Author: Jelena Telenius
Date: Fri Dec 29 14:35:40 2017 +0000
fp command out for portability, tester script mod for new location of ucsctools scripts
commit 608a6a7804919f9c4182e7d93d6a1e2d1fbdd495
Author: Jelena Telenius
Date: Tue Dec 19 15:24:47 2017 +0000
ucsctools and blat less conflict prone
commit 4361f3d21d6c5c6c9cd54f07fc97a3122ca5bc2c
Author: Jelena Telenius
Date: Tue Dec 19 14:17:52 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 scripts as blat, thus exporting ucsctools from the
conf/ucsctools instead
commit cb3d08e148a895e2e2682c6b56ddf33277a70515
Author: Jelena Telenius
Date: Wed Dec 13 13:02:26 2017 +0000
deleting outdated comments about adding new genomes
commit bb72822964e0930f21db2b70edd24cf104015ffe
Author: Jelena Telenius
Date: Fri Dec 8 12:26:22 2017 +0000
fixing version names
commit 5be98f6e0920967d4a993673ab0f0b255ca1415b
Author: Jelena Telenius
Date: Thu Nov 16 18:15:03 2017 +0000
ucsc genome sizes print to log file
commit 32100d2e57aa5809a6a5c31cc5c5a7a1e010aec7
Author: Jelena Telenius
Date: Thu Nov 16 17:01:39 2017 +0000
updating readme
commit 5cdf14a30337ac6f86dcf32a89d8187b6301dda8
Author: Jelena Telenius
Date: Thu Nov 16 16:43:09 2017 +0000
analyseMappedReads.pl help command update
commit 657e6f93644d91263c962d9a65d7de1e07c6a678
Author: Jelena Telenius
Date: Thu Nov 16 15:33:04 2017 +0000
Downgrading to stable version - dev moving to Cb5
commit 5b1120f69bb1ff54b39405dd86ec16344e674830
Author: Jelena Telenius
Date: Wed Nov 8 17:05:56 2017 +0000
Adding support to "all tools already in path" run mode
commit 78118350bce2df63366548ab679b62f8c8e2b2cb
Author: Jelena Telenius
Date: Wed Nov 8 16:37:19 2017 +0000
Portability fix : server path and server type weren't portable yet
commit 3d7b2548044e2eace2abd61aa67acf515833ccb1
Author: Jelena Telenius
Date: Wed Nov 1 14:16:14 2017 +0000
qmin parameter bug fix (for read trimming)
commit ae43714b48017ef327858269b6c00170a18e462a
Author: Jelena Telenius
Date: Wed Nov 1 11:38:07 2017 +0000
bug fix : Bowtie2 runs were always trimmed as PHRED64
commit 6b1275bb5bce3085b13722544ddb7b296f87d696
Author: Jelena Telenius
Date: Tue Oct 31 16:14:22 2017 +0000
Fixing filter.sh (generated bug when portability fixing)
configuration files in filter.sh were pointing to the old locations
commit 846145fcef39fc0a3298a85f2d5fa065d92f98fa
Author: Jelena Telenius
Date: Fri Oct 27 16:49:32 2017 +0100
Finalising tester script for portable release
commit fae6537525df6979b2f3113687ec462554bd182b
Author: Jelena Telenius
Date: Fri Oct 27 14:13:07 2017 +0100
Dividing config to 3 files, adding testEnvironment.sh
commit 3e0835806f0a8c18b43faa8df82b2b98520342c0
Author: Jelena Telenius
Date: Wed Oct 25 15:27:28 2017 +0100
Create LICENSE
commit 403903b767b261531e93ebf424e77c7a62381a3a
Author: Jelena Telenius
Date: Wed Oct 25 15:25:31 2017 +0100
Update README.md
commit 90c8189d49df149d25d5f6e99bfe8277ea6ceee4
Author: Jelena Telenius
Date: Wed Oct 25 15:23:33 2017 +0100
Intial commit : how the code was 25Oct2017
commit 2cae7d079ca91135fa242d924fbed9e89f58ae08
Author: Jelena Telenius
Date: Wed Oct 25 15:21:35 2017 +0100
Initial commit