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Forum: Bioinformatics 08-18-2017, 04:21 AM
Replies: 0
Views: 922
Posted By Hiroki
Unhappy Problem installing HTSeq on MacOS

Hi

I am trying to install HTSeq on MacOS El Capitan (10.11.6) like this:
pip install htseq --user

Then I got the following error message:
htslib/cram/cram_io.c:60:10: fatal error: 'lzma.h'...
Forum: Bioinformatics 12-05-2012, 04:27 PM
Replies: 2
Views: 2,334
Posted By Hiroki
Hi zinky, Thanks for the suggestion. I...

Hi zinky,

Thanks for the suggestion. I installed fastx-toolkit.
Although I needed to fix some script for some reason, it is running at least on CLI.
Thank you so much:)
Forum: Bioinformatics 12-02-2012, 11:02 PM
Replies: 2
Views: 2,334
Posted By Hiroki
Boxplot on Galaxy: gnuplot error?

Hi,
I am running a local Galaxy server on Mac. I tried to draw a boxplot from summary statistics created from groomed fastq data.

Then I got error message as follows:
An error occurred running...
Forum: Bioinformatics 11-24-2012, 10:46 PM
Replies: 19
Views: 4,427
Posted By Hiroki
GenoMax, yaximik and everybody, It worked...

GenoMax, yaximik and everybody,

It worked finally. Thank you soooo much:)
Forum: Bioinformatics 11-24-2012, 06:19 AM
Replies: 19
Views: 4,427
Posted By Hiroki
Hi yaximik, Thanks. I checked the wiki and...

Hi yaximik,

Thanks.
I checked the wiki and found that "Upload directory of files" seems to be the one I need. But when I open "Upload files" window, "Upload option" pull-down menu gives only two...
Forum: Bioinformatics 11-21-2012, 10:23 PM
Replies: 19
Views: 4,427
Posted By Hiroki
Hi yaximik, It worked:) Finally I could...

Hi yaximik,

It worked:) Finally I could become admin.
I created a new libraries and tried to add data to the library,
But then it was very slow or no progress...

So should I change the...
Forum: Bioinformatics 11-21-2012, 04:58 AM
Replies: 19
Views: 4,427
Posted By Hiroki
As bfantinatti did, I edited universe_wsgi.ini by...

As bfantinatti did, I edited universe_wsgi.ini by adding my email address and of course removed # from the line.
I reload run.sh and tried to log in with my email address. But it says "no such...
Forum: Bioinformatics 11-21-2012, 02:21 AM
Replies: 19
Views: 4,427
Posted By Hiroki
Hi guys, Thanks. So I understand I must to...

Hi guys,

Thanks. So I understand I must to be admin user to handle large files on Galaxy.
But like bfantinatti, I still don't know how to be admin user....
Forum: Bioinformatics 11-20-2012, 02:00 AM
Replies: 19
Views: 4,427
Posted By Hiroki
Hi, I have a very similar problem (uploading...

Hi,
I have a very similar problem (uploading fastq on my local GALAXY server taking extremely slow).
Was your problem solved, bfantinatti?? If so, how??
Forum: Bioinformatics 09-26-2012, 08:58 PM
Replies: 4
Views: 1,117
Posted By Hiroki
Hi maubp, Thanks a lot:)

Hi maubp,

Thanks a lot:)
Forum: Bioinformatics 09-18-2012, 12:40 AM
Replies: 4
Views: 1,117
Posted By Hiroki
Hi themerlin, Thanx a lot. I will try it. ...

Hi themerlin,

Thanx a lot.
I will try it.

Best,

Hiroki
Forum: Bioinformatics 09-17-2012, 08:18 PM
Replies: 4
Views: 1,117
Posted By Hiroki
Unhappy Combine pairend reads into one file for SOPRA

Hi there,

Sorry for a pitifully newbie question:confused:.

How can I combine two fasta files, read 1 and read2 from a Illumina pairend run into a single file as this:

>seq1read1...
Forum: Bioinformatics 07-12-2012, 10:48 PM
Replies: 252
Views: 106,409
Posted By Hiroki
Hi Boetsie, I emailed you some files a...

Hi Boetsie,

I emailed you some files a couple days ago.
Did you receive them?
Let me know if anything wrong.

Sorry if I'm rushing you...

Thanks.
Forum: Bioinformatics 07-11-2012, 01:33 AM
Replies: 252
Views: 106,409
Posted By Hiroki
Thanks for the response. I will PM you soon. ...

Thanks for the response.
I will PM you soon.

Hiroki
Forum: Bioinformatics 07-10-2012, 11:30 PM
Replies: 252
Views: 106,409
Posted By Hiroki
Hi boetsie, I am trying to make scaffold...

Hi boetsie,

I am trying to make scaffold from contigs from 454 data with Illumina mate pair 75-bp reads with different sizes.

There are 502k contigs and only 1000 or so decreased by...
Forum: Illumina/Solexa 01-30-2012, 11:54 PM
Replies: 6
Views: 17,762
Posted By Hiroki
Smile Thanks ulz_peter! I was told to use Picard...

Thanks ulz_peter!

I was told to use Picard from another guy.
Now I'm trying it.

Thank you so much anyways!
Forum: Illumina/Solexa 01-30-2012, 08:08 PM
Replies: 6
Views: 17,762
Posted By Hiroki
Changing header of BAM

Hello,

I apologize if my question is redundant....

I created bam files from fastq files by ELAND_standalone and tried to feed them to GATK. Then I got the following error message.
##### ERROR...
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