CCseqBasic4 code changes log file
This log was Last updated by Jelena :
Mon Oct 8 16:56:53 BST 2018
commit 50f9fcd51b17afaf60b163eb55a2d2621d960b23
Author: telenius
Date: Fri Jul 6 15:16:41 2018 +0100
fix to earlier fix
commit cdd9b1ed6708591081401adf2f7ff6fb0eeb5207
Author: telenius
Date: Fri Jul 6 12:19:31 2018 +0100
fix of accidental revert of code
plus intra-WIMM user support to public area
commit 09230a4def443988c393535c3a0d7dbee2513928
Author: telenius
Date: Fri Jul 6 11:59:15 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 43189be4d6cc2be0640dad15f36f349375ae4059
Author: telenius
Date: Mon Jun 25 11:25:18 2018 +0100
catching error status of filtering
commit 2ae4a8500ef75d9a2d61870b6110d5cf90d08226
Author: telenius
Date: Tue Jun 19 10:39:23 2018 +0100
fixing name of generated RE cut genome file
commit fe0bb106fd4b306d002b46ecb4e3f8d5deb7db5b
Author: telenius
Date: Wed May 30 12:11:00 2018 +0100
fix to yesterdays fix
commit de8958aff84e4a34735991e58c8c314ec4dce50f
Author: telenius
Date: Wed May 30 12:07:21 2018 +0100
fix to yesterdays fix
commit 8e2b6651687328e9ccd2e8b386bfcfff12e263d5
Author: telenius
Date: Tue May 29 17:10:04 2018 +0100
fixing bowtie1 -v flag
commit 177a67f3884248b9e1dc8e101887ea300c1e5f13
Author: telenius
Date: Fri May 11 16:04:28 2018 +0100
hindIII genome cutter fix
commit 6c8ab6749af17c3315cfd6d5dbbc2aae590e12d6
Author: telenius
Date: Fri May 4 20:07:37 2018 +0100
fixing bowtie -v flag
commit 6e5a07308878fc22dabedcfe9b9ea76e9ecda1ee
Author: Jelena Telenius
Date: Fri Mar 9 15:25:52 2018 +0000
cleaning up harmless track creation warnings
commit 158eff8dbd61f588d80b80e01501c37b602e0438
Author: Jelena Telenius
Date: Thu Mar 8 19:44:03 2018 +0000
fastqc version upgrade, samtools sort version upgrade
commit 7e2e94fa63bc4610dcb1f26057a7c90fd37d9ba1
Author: Jelena Telenius
Date: Mon Mar 5 18:45:56 2018 +0000
typo correction in output log on-the-fly hub addresses
commit 63387cfcd59389c08f8b502824727a7af8d1639f
Author: Jelena Telenius
Date: Mon Mar 5 15:04:36 2018 +0000
figure make fix : flash log parse to support new versions of flash
commit 898a22913ef60ae2d97385eb65a662379ec895d5
Author: Jelena Telenius
Date: Thu Mar 1 16:12:09 2018 +0000
added a note about ucstools
commit 75108900a9413c4fd80970f0747ccd5920ecc315
Author: Jelena Telenius
Date: Thu Mar 1 16:03:48 2018 +0000
Update README.md
commit bdb6b723f7c9696f134acfc97f10bb4f0c6f76c3
Author: Jelena Telenius
Date: Thu Mar 1 15:15:53 2018 +0000
Update README.md
commit 0b14435793a2f396e609df0918ac0240e65a34e2
Author: Jelena Telenius
Date: Mon Feb 26 13:46:38 2018 +0000
Disabling the makeSymbolicLinks subroutine : no symlinks in public from now on
commit e6ef4d0cc892eb4911b39f683c9cfb35fa14b498
Author: Jelena Telenius
Date: Mon Feb 19 11:04:14 2018 +0000
genomes.txt file portability bug fix
commit 432de75c035891852acfb2482b9abee04176748b
Author: Jelena Telenius
Date: Mon Jan 8 14:55:10 2018 +0000
still one more fp : fix for portability
commit 2e0213663ca02dd2c5b5903a47768992d0dc6a39
Author: Jelena Telenius
Date: Wed Jan 3 18:21:56 2018 +0000
typo correction in the oligo file portability fix
commit eb95a1e725077c6071513d8e2472c7223f9a645a
Author: Jelena Telenius
Date: Fri Dec 29 14:36:01 2017 +0000
fp command out for portability, tester script mod for new location of ucsctools scripts
commit dc8a809cfb3b000550fed5a960aafd4800a85318
Author: Jelena Telenius
Date: Tue Dec 19 15:25:03 2017 +0000
ucsctools and blat less conflict prone
commit b646f4d6abaca53cb305d114115b9beb2f257eea
Author: Jelena Telenius
Date: Tue Dec 19 14:18:34 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 2886169b37e0f2895f5a2b4ca77c6188a790c712
Author: Jelena Telenius
Date: Wed Dec 13 13:03:02 2017 +0000
deleting outdated comments about adding new genomes
commit bf28d51121a3f731012cef8cc09f58c9f7b0ebf8
Author: Jelena Telenius
Date: Fri Dec 8 12:17:36 2017 +0000
fix version names again
commit 90066336a59276bf9ec5a543ebcd2b294d26921d
Author: Jelena Telenius
Date: Fri Dec 8 11:32:17 2017 +0000
version name typo fix in analyseMappedReads.pl
commit 40ec475e3e913634fa71cd325768ada68e8f58cd
Author: Jelena Telenius
Date: Thu Nov 16 18:15:35 2017 +0000
ucsc genome sizes print to log file
commit e9f22af94c44bf41d3045a71740bee8a49e0c4fa
Author: Jelena Telenius
Date: Thu Nov 16 17:01:05 2017 +0000
updating readme
commit 8c0698d3835bb16080438e5521612a0c00d853d2
Author: Jelena Telenius
Date: Thu Nov 16 16:43:42 2017 +0000
analyseMappedReads.pl help command update
commit 8b54d738d206de7a234f7843004b9ec60250af51
Author: Jelena Telenius
Date: Thu Nov 16 15:33:51 2017 +0000
Downgrading to stable version - dev moving to Cb5
commit 955d1fd0d856f69c904ac54495d069e6aa8cb145
Author: Jelena Telenius
Date: Wed Nov 8 17:04:45 2017 +0000
Adding support to "all tools already in path" run mode
commit 087704ffb1fcde8922cf797de874d13b7b26e5b6
Author: Jelena Telenius
Date: Wed Nov 8 16:38:46 2017 +0000
Portability fix : server path and server type weren't portable yet
commit 17ccca254da58f7297978f6c4a75f117727a2953
Author: Jelena Telenius
Date: Wed Nov 8 15:02:51 2017 +0000
removing old config file
commit 21cea233682583fa788498c34003cdc2831e2987
Author: Jelena Telenius
Date: Wed Nov 1 13:49:59 2017 +0000
first try to UMI support - not fully functional yet
commit 9281666c88f2cc4f70a7713a2cb6e18643748e53
Author: Jelena Telenius
Date: Wed Nov 1 13:46:26 2017 +0000
bowtie2 support - genome setup bug fixes
commit 6ee25d185be9796ff1ca0ae3b956d418f65d8beb
Author: Jelena Telenius
Date: Wed Nov 1 11:37:31 2017 +0000
bug fix : Bowtie2 runs were always trimmed as PHRED64
commit a409dc40d5c702c707bf5608384c543e4fe844a9
Author: Jelena Telenius
Date: Tue Oct 31 16:12:30 2017 +0000
Fixing filter.sh (generated bug when portability fixing)
configuration files in filter.sh were pointing to the old locations
commit ed5b99fd7c7c83e78cd6bbd87a424f082bbc4109
Author: Jelena Telenius
Date: Fri Oct 27 16:51:20 2017 +0100
Finalising tester script for portable release
commit 293c15ab7c40ba3dce062d1732eba81a2a754956
Author: Jelena Telenius
Date: Fri Oct 27 14:00:11 2017 +0100
Edit of setup instructions
commit 4e0173e545c017d7e135fbda8d95ad1dc8e58236
Author: Jelena Telenius
Date: Fri Oct 27 13:49:46 2017 +0100
Re-add all files ( and recent updates to code )
Dividing the config file to 3 parts, adding testEnvironment.sh script to make installation easier.
These should be only small changes in the code, but as all the files vanished because funny commit,
this commit looks like a lot.
commit 62f5b2d56716d102399373488e43d6919c126398
Author: Jelena Telenius
Date: Fri Oct 27 13:36:35 2017 +0100
Revert "config file to 3 parts, testEnvironment.sh created"
This reverts commit 205b98cf607936be36e950cf9b7cd05143b00a50.
commit 205b98cf607936be36e950cf9b7cd05143b00a50
Author: Jelena Telenius
Date: Fri Oct 27 13:12:12 2017 +0100
config file to 3 parts, testEnvironment.sh created
commit f845d86d90a6783951aea5d08a9231f7de63e969
Author: Jelena Telenius
Date: Wed Oct 25 15:26:33 2017 +0100
Update README.md
commit 6fee50719cf9b4275bf78651419dbf225f07e30a
Author: Jelena Telenius
Date: Wed Oct 25 15:26:20 2017 +0100
Initial commit