Link files from another disk to my local Galaxy instance

Question: Link files from another disk to my local Galaxy instance

3.7 years ago by

Brazil

Guilherme Dias • 110 wrote:

I was trying to use the tool "Upload files from filesystem paths" to link some .fastq files to my local Galaxy installation. These fastq files were in a different disk from the Galaxy installation and, although using the complete path to the files, I kept getting the error: "invalid paths".

Once I copied the files to the same disk as Galaxy (and altered the path accordingly), the link was successfully executed.

Why couldn't I link to files present in another disk?

upload link filesystem path • 928 views

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modified 3.1 years ago by juls.jaeger • 10 • written 3.7 years ago by Guilherme Dias • 110

3.1 years ago by

juls.jaeger • 10

United Kingdom

juls.jaeger • 10 wrote:

Hi, problem solved. I added the data as 'Upload directory of files'.

cheers, Julian

ADD COMMENT • link written 3.1 years ago by juls.jaeger • 10

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Just to confirm, you are loading into Data Libraries using this protocol? http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

If so, it could be that you have more than one symbolic link in the path. Galaxy will resolve only one.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hey Jen,

I'm not sure if i'm following what you said. The directory contains only two files (paired-end reads R1 and R2).
So I just typed the path to each of the files:

/media/mcclintock/Banco de dados/Guilherme/Data/Intensities/BaseCalls/Dseriema_S1_L001_R1_001.fastq
/media/mcclintock/Banco de dados/Guilherme/Data/Intensities/BaseCalls/Dseriema_S1_L001_R2_001.fastq

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by Guilherme Dias • 110

Hello - sorry I missed this before - and maybe you have solved it, but the paths appear to contain spaces. This would be a problem. If there really are spaces, then try quoting the path.

Thanks, Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

3.1 years ago by

juls.jaeger • 10

United Kingdom

juls.jaeger • 10 wrote:

Hi, I have the same problem. Galaxy changes my upload filepath

file:///media/julian/myDATA/201509028_RNAseq%20rawdata/WTCHG_212999_209_1.fastq

to Invalid paths: "/home/julian/galaxy/file:/media/julian/myDATA/201509028_RNAseq%20rawdata/WTCHG_212999_209_1.fastq".

It should be possible to link files into the library from other paths then the galaxy directory, or?

Thanks for any help, Julian

ADD COMMENT • link written 3.1 years ago by juls.jaeger • 10

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