Hello Chetan,

Björn sent you a different link yesterday. Please read through it - especially this part: Upload files from filesystem paths.

https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

M.

On Tue, Feb 25, 2014 at 5:37 AM, do kadya <dokadya@gmail.com> wrote:

Hi,

Thank You for reply.

I am still not clear about this website.

https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP

There are total 4 main points highlighted in this website.

Do I have to follow all 4 points ?

I have tried just on second point which is 

Configuring Galaxy

As I just need same folder for galaxy where I can put my content directly.

Now after sometime I will all of the points mentioned.

Next Question is WHY GALAXY IS NOT ACCEPTING .bai files?

.bai is indexed form of .bam files.

I tried uploading using admin section upload, which not worked.

next normal file upload as .bai file is just 6 MB., but not worked.

next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB.

in all of my try .bai file is 0 KB.

I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM.

 

Waiting for positive reply.

On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi Do,

the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy.
As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho.

Cheers,
Bjoern

Hi,
Thank You for answers, I am able to learn everyday.

I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy
for local lab purpose.
'x' tool require bam files which are of 400 GB file size. When I used Admin
section to upload file my computer hang because of no space.

Is it way that I can tell Galaxy that use these files directly or may be I
can convert files to Galaxy required format so that galaxy will not create
files by itself.

As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM
files, replication of data by Galaxy its not possible for me.

Some option like tell Galaxy about extension and properties of file, so
that it should not replicate.

By command line 'x' is working fine.


Need some really good solution.
Waiting for positive reply.
Thank You.
--
Reagrds,
Chetan
dokadya@gmail.com

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Regards,

Chetan

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