10 most Recent Topics

10 most Recent Topics - UGENE Forum http://ugene.unipro.ru/forum/YaBB.pl - UGENE Forum en-us UGENE Forum Sat, 19 May 2012 03:55:15 +0000 http://blogs.law.harvard.edu/tech/rss 30 Feature Requests - Please add ppa support to Ubuntu 12.04 ("Precise" series) http://ugene.unipro.ru/forum/YaBB.pl?num=1336756561/1#1 UGENE Forum/Feature Requests http://ugene.unipro.ru/forum/YaBB.pl?num=1336756561/1#1 Hi, Alvarenga. There's no need to add the "ppa:iefremov/ppa". Just make sure you have other sources enabled and you'll find Ugene in the software center. It's outdated but you get the integration you mentioned. Then you need to extract the newer version to the folder (/usr/lib64/ugene, for the 64 bits version) and that's all (you have to make it as root, so from terminal: 'gksu nautilus', then search and open the ugene compressed file and extract to /usr/lib64/ugene, unless you use the 32 bits, in which case I guess is lib32 or maybe just lib, not sure). To enable other sources in ubuntu: search for the update manager, click Settings (bottom left) and then in other sources, check canonical partners (see screenshot attached). Help and How-to - Amino Acids Color Scheme http://ugene.unipro.ru/forum/YaBB.pl?num=1337064665/1#1 UGENE Forum/Help and How-to http://ugene.unipro.ru/forum/YaBB.pl?num=1337064665/1#1 Hi, I've created a new issue to allow one to customize a multiple alignment's color scheme. So you would be able to set up the specified scheme as well as any other required scheme as soon as this issue is implemented. You can track the issue status here: <a href="https://ugene.unipro.ru/tracker/browse/UGENE-993" target="_blank">https://ugene.unipro.ru/tracker/browse/UGENE-993</a> Help and How-to - Problem running 64bit linux ugene http://ugene.unipro.ru/forum/YaBB.pl?num=1333979695/4#4 UGENE Forum/Help and How-to http://ugene.unipro.ru/forum/YaBB.pl?num=1333979695/4#4 Hi, Rosz. Did you have an older version working? I ask you that because I had a similar problem in ubuntu, and the solution was to delete all the files in the previous version before extracting the new files to that folder. So, if your working ugene is in /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ Then try deleting everything in that folder and then extract the new files (directly to the ugene folder and not creating a subfolder like 'ugene-1.10.4'). Feature Requests - Show enzymes that don't cut http://ugene.unipro.ru/forum/YaBB.pl?num=1336400222/2#2 UGENE Forum/Feature Requests http://ugene.unipro.ru/forum/YaBB.pl?num=1336400222/2#2 Thanks, that is what I was after - to find a group of enzymes that don't cut the sequence. I don't often use the circular view, which is why I hadn't spotted it before. I guess a more minor suggestion, then, would be whether the enzymes that don't cut could be included in the linear view. When I select 'Actions-Analyze-Find restriction sites' there's an option for minimum hits, which can be set to zero, although enzymes with zero hits don't show up in the linear results. I'd also like to be able to save the list of enzymes to compare with hits from another sequence, i.e. find a list of enzymes that cut neither sequence. Bugs and Issues - Can't use latest linux 32-bit full version http://ugene.unipro.ru/forum/YaBB.pl?num=1336304790/2#2 UGENE Forum/Bugs and Issues http://ugene.unipro.ru/forum/YaBB.pl?num=1336304790/2#2 Oh, it seems, you were right - I redownloaded it and everything worked well! Thank you!  <img src="http://ugene.unipro.ru/yabbfiles/Templates/Forum/yabb21/smiley.gif" border="0" alt="Smiley" title="Smiley" /> Bugs and Issues - Issue with LUCY http://ugene.unipro.ru/forum/YaBB.pl?num=1335406588/0#0 UGENE Forum/Bugs and Issues http://ugene.unipro.ru/forum/YaBB.pl?num=1335406588/0#0 Hi there, I'm not sure what is the problem behind the execution of LUCY in the UGENE with cusstom CMDline tool. Please see screenshots for the details. Thanks! Kenneth Bugs and Issues - MUSCLE Alignment of Nucleotides Crashes in 64-bit Win7 http://ugene.unipro.ru/forum/YaBB.pl?num=1334759037/4#4 UGENE Forum/Bugs and Issues http://ugene.unipro.ru/forum/YaBB.pl?num=1334759037/4#4 Okay, I downloaded the latest development package, and it too crashed. The info generated by UGENE is below and also sent via crash reporter control. =========================== Exception with code c0000005 - Access violation::143ce5f Operation system: Windows x86 UGENE version: 1.11.0-dev ActiveWindow: None Log: [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, factory: SQLiteDbi [16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_0.ugenedb, ref-count: 1 [16:06:18.835] [Tasks] Registering new task: Export sequence to document [16:06:18.849] [Tasks] promoting task {Export sequence to document} to 'Prepared' [16:06:18.849] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Prepared' [16:06:18.849] [Tasks] promoting task {Export sequence to document} to 'Running' [16:06:18.849] [Tasks] acquiring resource: 'Threads':1, state: 1/1000 [16:06:18.849] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Running' [16:06:18.881] [Tasks] releasing resource: 'Threads':1, state: 0/1000 [16:06:18.882] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Finished' [16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Prepared' [16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Running' [16:06:18.882] [Core Services] Adding document to the project: Z:/service.web.abiyotek/UGENE/RefStandards.aln [16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Finished' [16:06:18.882] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Prepared' [16:06:18.882] [Core Services] Starting load document from Z:/service.web.abiyotek/UGENE/RefStandards.aln, document format CLUSTALW [16:06:18.882] [Core Services] resource 'Project Document::Z:/service.web.abiyotek/UGENE/RefStandards.aln' is used by 'Load 'RefStandards.aln'' [16:06:18.882] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Prepared' [16:06:18.882] [Core Services] load document:Memory resource 0 [16:06:18.882] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Prepared' [16:06:18.882] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Running' [16:06:18.882] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Running' [16:06:18.882] [Tasks] acquiring resource: 'Threads':1, state: 1/1000 [16:06:18.882] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Running' [16:06:18.892] [Tasks] releasing resource: 'Threads':1, state: 0/1000 [16:06:18.892] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Finished' [16:06:18.892] [Core Services] resource 'Project Document::Z:/service.web.abiyotek/UGENE/RefStandards.aln' is released by 'Load 'RefStandards.aln'' [16:06:18.892] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Finished' [16:06:18.922] [Tasks] promoting task {Open view} to 'Prepared' [16:06:18.928] [Tasks] promoting task {Open new 'Alignment editor'} to 'Prepared' [16:06:18.928] [Tasks] promoting task {Open view} to 'Running' [16:06:18.928] [Tasks] promoting task {Open new 'Alignment editor'} to 'Running' [16:06:18.982] [Tasks] promoting task {Open new 'Alignment editor'} to 'Finished' [16:06:18.982] [Tasks] promoting task {Open view} to 'Finished' [16:06:18.982] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Finished' [16:06:19.067] [Tasks] promoting task {Export sequence to document} to 'Finished' [16:06:19.067] [Tasks] Unregistering task: Export sequence to document [16:06:19.067] [Tasks] Deleting task: Export alignment to 'RefStandards.aln' [16:06:19.067] [Tasks] Deleting task: Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln [16:06:19.067] [Tasks] Deleting task: Read document: 'RefStandards.aln' [16:06:19.067] [Tasks] Deleting task: Load 'RefStandards.aln' [16:06:19.067] [Tasks] Deleting task: Open new 'Alignment editor' [16:06:19.067] [Tasks] Deleting task: Open view [16:06:19.067] [Tasks] Deleting task: Load document: 'RefStandards.aln' [16:06:19.067] [Tasks] Deleting task: Export sequence to document [16:06:31.626] [Tasks] Registering new task: MUSCLE align 'RefStandards.aln' [16:06:31.667] [Tasks] promoting task {MUSCLE align 'RefStandards.aln'} to 'Prepared' [16:06:31.667] [Tasks] Starting {MUSCLE align 'RefStandards.aln'} task [16:06:31.668] [Tasks] promoting task {Workflow wrapper 'MUSCLE align 'RefStandards.aln''} to 'Prepared' [16:06:31.669] [Tasks] promoting task {Run workflow: align} to 'Prepared' [16:06:31.669] [Tasks] promoting task {Save document} to 'Prepared' [16:06:31.669] [Tasks] promoting task {MUSCLE align 'RefStandards.aln'} to 'Running' [16:06:31.669] [Tasks] promoting task {Workflow wrapper 'MUSCLE align 'RefStandards.aln''} to 'Running' [16:06:31.669] [Tasks] promoting task {Run workflow: align} to 'Running' [16:06:31.669] [Tasks] acquiring resource: 'Threads':1, state: 1/1000 [16:06:31.669] [Tasks] promoting task {Save document} to 'Running' [16:06:31.672] [Core Services] Saving document C:/Users/mitch/AppData/Local/Temp/c10260.fasta [16:06:31.672] [Tasks] releasing resource: 'Threads':1, state: 0/1000 [16:06:31.672] [Tasks] promoting task {Save document} to 'Finished' [16:06:31.675] [Core Services] Starting UGENE workflow: C:/Program Files/Unipro UGENE/ugene.exe --task=data:cmdline/align.uwl --log-no-task-progress --ugene-output-progress-state --lang=en --ugene-output-error --ini-file="C:/Users/mitch/AppData/Roaming/Unipro/UGENE.ini" --mode=0 --max-iterations=8 --stable=1 --in=C:/Users/mitch/AppData/Local/Temp/c10260.fasta --out=C:/Users/mitch/AppData/Local/Temp/K10260.fasta --format=fasta --log-level-details Task tree: MUSCLE align 'RefStandards.aln'      (Running)      49 -Workflow wrapper 'MUSCLE align 'RefStandards.aln''      (Running)      49 --Run workflow: align      (Running)      49 ---Workflow process      (New)      -1 OS-Version: 6.1.7601 (Service Pack 1) 0x300-0x1 0x143ce5f: (U2Lang.dll) ?prepare:RunCmdlineWorkflowTask:U2::UAEXXZ + 0x90f 0x329ac0: (U2Private.dll) ?append:?$QList:PAVPluginRef:U2::::QAEXABQAVPluginRef:U2:::Z + 0x60 0x32d728: (U2Private.dll) ?addToPriorityQueue:TaskSchedulerImpl:U2::AAE_NPAVTask:2:PAVTaskInfo:2::Z + 0x158 0x32d91d: (U2Private.dll) ?processNewSubtasks:TaskSchedulerImpl:U2::AAEXXZ + 0xbd 0x32dc1e: (U2Private.dll) ?update:TaskSchedulerImpl:U2::AAEXXZ + 0x2e 0x32e238: (U2Private.dll) ?qt_metacall:TaskSchedulerImpl:U2::UAEHW4Call:QMetaObject::HPAPAX:Z + 0x48 0x32e238: (U2Private.dll) ?qt_metacall:TaskSchedulerImpl:U2::UAEHW4Call:QMetaObject::HPAPAX:Z + 0x48 Bugs and Issues - GPU-Blast error http://ugene.unipro.ru/forum/YaBB.pl?num=1335148066/1#1 UGENE Forum/Bugs and Issues http://ugene.unipro.ru/forum/YaBB.pl?num=1335148066/1#1 Hi, besides that I'm getting this unknown "error" (screenshot) Not sure why, tries to execute the workflow, it ended but the log doesn't shows that. Bugs and Issues - ugene 1.10.4 crash http://ugene.unipro.ru/forum/YaBB.pl?num=1334329614/4#4 UGENE Forum/Bugs and Issues http://ugene.unipro.ru/forum/YaBB.pl?num=1334329614/4#4 Hi, sorry for late...yes i sent the crash report many times both linux and windows...the crash event is not immediate but after few minutes that the file is opened. thanks max Feature Requests - BLAST input file types http://ugene.unipro.ru/forum/YaBB.pl?num=1335151539/0#0 UGENE Forum/Feature Requests http://ugene.unipro.ru/forum/YaBB.pl?num=1335151539/0#0 Hi there, Is it possible to make BLAST to accept "Output URL file" from an external tool custom element? I'm integrating LUCY tool in the UGENE WD, and realizes that the data will not parse if I set the output file type as "Output URL file", however when I set it as FASTA the data was successfully parsed into the BLAST element. However in the BLAST element the input sequence cannot be selected as the output from LUCY. Kindly advice. Thanks! Kenneth