Upload fastq to 'Data Libraries' Using Bioblend Python library

Question: Upload fastq to 'Data Libraries' Using Bioblend Python library

2.4 years ago by

amey.damle • 30 wrote:

Hello , I am a Developer from INDIA , I am using the galaxy API to create a library,upload fast files, run the workflow and get the output of each fastq files. for that I am using the python library of http://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries , now I am stuck in uploading the fastq files. means creating the datasets. When I used this upload_file_from_server function , it uploads all the files from the given directory. I do not want to upload all the files only fastq files expected. that's my problem in this. when I use upload_file_from_url , for each files giving the file path but it creates` something else in Data library.

can anyone please help me out for this.

fastq galaxy python • 899 views

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modified 2.4 years ago by Hotz, Hans-Rudolf • 1.8k • written 2.4 years ago by amey.damle • 30

What is the "something else" that it creates in the data library when you select to paste links?

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by Peter van Heusden • 150

2.4 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

have you tried identifying the fastq files in the given directory first, loop over them, and then use: "upload_file_from_local_path" or "upload_from_galaxy_filesystem" ?

Hans-Rudolf

ADD COMMENT • link written 2.4 years ago by Hotz, Hans-Rudolf • 1.8k

Hi , yes i tried but my fastq file are not in local path , it is in the another server. and using 'upload_file_from_server i am able to upload but the uploaded files response is something 'pasted Entry'. Please help me to upload the fastq as datasets and run the workflow with the datasets inputs.

ADD REPLY • link written 2.4 years ago by amey.damle • 30

I can't follow your comment: Are the files on a different filesystem which is not accesible by the Galaxy server? if 'yes': you need to copy them anyway, if 'no': "upload_file_from_local_path" will work

ADD REPLY • link written 2.4 years ago by Hotz, Hans-Rudolf • 1.8k

No , that files are in the same filesystem where the galaxy placed. and the file are accesible by the galaxy. i can not copy the files into local file system because they are too large as you knew the fastq files.

ADD REPLY • link written 2.4 years ago by amey.damle • 30

So, why does "upload_file_from_local_path" not work for you then?

ADD REPLY • link written 2.4 years ago by Hotz, Hans-Rudolf • 1.8k

because the upload_file_from_local_path function is searching for files in my local machine. it giving me error of No such file or directory found.

What to do ?

ADD REPLY • link written 2.4 years ago by amey.damle • 30

I am sorry, again, I don't understand:

what is "local machine" ? Is this not your galaxy server? what happens if you run your python script on the galaxy server?

ADD REPLY • link written 2.4 years ago by Hotz, Hans-Rudolf • 1.8k

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