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Forum: Bioinformatics 10-20-2016, 06:32 PM
Replies: 12
Views: 15,192
Posted By RDW
Where are you trying to run it from? The missing...

Where are you trying to run it from? The missing dll suggests you might be trying to use it from (e.g.) the Windows command prompt rather than the Cygwin bash shell, which complicates things a lot....
Forum: Bioinformatics 04-10-2014, 02:43 PM
Replies: 7
Views: 3,071
Posted By RDW
Thanks for the quick response! Is...

Thanks for the quick response!

Is TRgamma/delta now supported?- I see a patch for this was mentioned on Biostars a few months ago.
Forum: Bioinformatics 04-10-2014, 09:51 AM
Replies: 7
Views: 3,071
Posted By RDW
One problem is that the website seems to be...

One problem is that the website seems to be broken. :)
Forum: Bioinformatics 03-26-2014, 06:44 AM
Replies: 8
Views: 3,766
Posted By RDW
Since this thread was started, a 64-bit version...

Since this thread was started, a 64-bit version of Cygwin ( http://www.cygwin.com/ ) has been released. It can certainly build bwa from the latest source at http://bio-bwa.sourceforge.net/ but I...
Forum: Bioinformatics 10-30-2013, 06:39 AM
Replies: 3
Views: 1,682
Posted By RDW
EMBOSS restrict?: ...

EMBOSS restrict?:

http://emboss.sourceforge.net/
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/restrict.html
Forum: Bioinformatics 10-28-2013, 02:33 PM
Replies: 4
Views: 1,062
Posted By RDW
perl -pe 's/^>.+(GroupUn.+),.+/>$1/' in.fasta...

perl -pe 's/^>.+(GroupUn.+),.+/>$1/' in.fasta >out.fasta
Forum: Bioinformatics 10-28-2013, 09:40 AM
Replies: 7
Views: 3,952
Posted By RDW
perl -pe 'chomp;s/>.+//' input.fasta...

perl -pe 'chomp;s/>.+//' input.fasta >out.txt
Forum: Bioinformatics 05-23-2013, 09:21 AM
Replies: 7
Views: 2,013
Posted By RDW
If you downloaded samtools from the official...

If you downloaded samtools from the official samtools page on Sourceforge, you probably just got source code, which is hard to use on Windows. However, there's an unofficial executable version for...
Forum: Bioinformatics 01-30-2013, 04:53 PM
Replies: 6
Views: 8,184
Posted By RDW
As far as I recall, it can't. Time to upgrade the...

As far as I recall, it can't. Time to upgrade the OS!
Forum: Bioinformatics 07-13-2012, 07:53 AM
Replies: 3
Views: 1,758
Posted By RDW
http://www.ebi.ac.uk/training/handson/

http://www.ebi.ac.uk/training/handson/
Forum: Bioinformatics 06-14-2012, 10:21 AM
Replies: 9
Views: 2,895
Posted By RDW
ANNOVAR can also accept text files - see my link....

ANNOVAR can also accept text files - see my link. You just need an extra column that duplicates the variant position (since for SNPs, the start position is the same as the end). Any program that can...
Forum: Bioinformatics 06-13-2012, 11:00 AM
Replies: 3
Views: 2,044
Posted By RDW
You probably want to use GATK's scatter/gather...

You probably want to use GATK's scatter/gather parallelism:

http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK

Their 'best practice' Queue script is set up to implement...
Forum: Bioinformatics 06-13-2012, 10:51 AM
Replies: 9
Views: 2,895
Posted By RDW
With a few lines of Perl (or equivalent) you can...

With a few lines of Perl (or equivalent) you can convert the MuTect output into something that ANNOVAR can read - I think ANNOVAR needs explicit start and end positions for the variant, even if these...
Forum: Bioinformatics 05-16-2012, 03:30 AM
Replies: 8
Views: 3,766
Posted By RDW
Good stuff! The binary works for me and glad to...

Good stuff! The binary works for me and glad to see the code.
Forum: Bioinformatics 04-24-2012, 11:54 AM
Replies: 15
Views: 9,282
Posted By RDW
Yes, clickthroughs are probably as legally...

Yes, clickthroughs are probably as legally enforceable as this:

http://xkcd.com/501/ :)



Sounds interesting - a lot of people would find this useful!
Forum: Bioinformatics 04-24-2012, 03:20 AM
Replies: 15
Views: 9,282
Posted By RDW
Hi Dong, I'm not familiar with Codeplex - is it...

Hi Dong, I'm not familiar with Codeplex - is it compulsory to have a clickthrough licence, or could you turn this feature off? You could comply with the GPL just by including the source in your zip...
Forum: Bioinformatics 04-23-2012, 03:59 AM
Replies: 15
Views: 9,282
Posted By RDW
It looks like the licence for this build needs to...

It looks like the licence for this build needs to be fixed. BWA is GPL3, but you are required to agree to the (GPL-incompatible) Microsoft Public Licence to download it.
Forum: Bioinformatics 03-06-2012, 02:19 PM
Replies: 15
Views: 9,282
Posted By RDW
I see that the Ugene guys have now added a 64-bit...

I see that the Ugene guys have now added a 64-bit Windows build of BWA 0.5.9 to the external tools package mentioned above:

http://ugene.unipro.ru/downloads/ext_tools_win_64-bit.zip
Forum: Bioinformatics 03-06-2012, 01:53 PM
Replies: 10
Views: 4,005
Posted By RDW
No problem running 24 threads on 12 physical...

No problem running 24 threads on 12 physical cores (dual 6-core Xeon X5690 with hyperthreading). Linux 2.6.35-32-generic #66-Ubuntu SMP (x86_64), BWA 0.5.9-r16.
Forum: Bioinformatics 03-05-2012, 08:04 AM
Replies: 10
Views: 5,644
Posted By RDW
Yes, what is it with SGE and fonts?! The...

Yes, what is it with SGE and fonts?! The witchcraft that eventually worked for me (with a recent Ubuntu) was installing the set of font packages listed in section 8.4.1 of this blog post (then...
Forum: Bioinformatics 03-03-2012, 09:29 AM
Replies: 10
Views: 5,644
Posted By RDW
Oh well, there goes that theory. It would be...

Oh well, there goes that theory. It would be interesting to hear how you get on with this - I don't think that many people outside Broad are using GATK-Queue.
Forum: Bioinformatics 03-02-2012, 05:40 PM
Replies: 10
Views: 5,644
Posted By RDW
I'm guessing that the tasks that did run in...

I'm guessing that the tasks that did run in parallel were using walkers that support GATK's 'shared memory parallelism' - i.e., the same ones that support the '-nt' thread option on the command line....
Forum: Bioinformatics 03-02-2012, 10:51 AM
Replies: 10
Views: 5,644
Posted By RDW
Have you tried the -jobRunner option and a...

Have you tried the -jobRunner option and a supported batch queuing system?:

http://www.broadinstitute.org/gsa/wiki/index.php/QFunction_and_Command_Line_Options

"The job runner to dispatch jobs....
Forum: Bioinformatics 02-15-2012, 07:34 AM
Replies: 12
Views: 4,372
Posted By RDW
One problem with Cygwin (and, the last time I...

One problem with Cygwin (and, the last time I checked, the bwa build in UGene) is that you are limited to 32-bit applications, which can be inadequate for many common NGS tasks. 64-bit Linux will be...
Forum: Bioinformatics 12-27-2011, 04:07 AM
Replies: 15
Views: 9,282
Posted By RDW
The UGENE version is still 32-bit, but they built...

The UGENE version is still 32-bit, but they built it without Cygwin dependencies, which is promising for a 64-bit build. Might be worth re-visiting this.
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