format for csv file to import a sequencing request sample
Hi, What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample? Thanks, Natalie
Natalie, The format of the csv file for importing samples depends on the sample form fields. For example if the sample for fields are: 1. Type (SelectField: DNA, total RNA) 2. Library (SelectField: Fragment, mate-pair) 3. Volume (TextField) 4. Concentration (TextField) Then in the scv file each row (for a sample) should look like: DNA,Fragment,0.22,24.7 rc On Mar 23, 2010, at 10:02 AM, nsfox@uwaterloo.ca wrote:
Hi,
What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample?
Thanks, Natalie
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
I've attempted this and I'm getting the Error message "Error in importing samples file". Here's the details of what I did: My Sequencing sample form specifies on grid level called "Sample Description" with the fields: "Sample Description", "Genus species", and "Comments". my csv file has only the line of text: Emerging Tassel (Male),Zea mays,test And all I did to import it is clicked browse within the sequencing request and selected the file, then I pressed import samples. Galaxy navigated back to the Sequencing Request page and there was the Error message in the top right corner and the sample wasn't imported. Thanks for the help, Natalie Quoting Ramkrishna Chakrabarty <rc@bx.psu.edu>:
Natalie,
The format of the csv file for importing samples depends on the sample form fields. For example if the sample for fields are: 1. Type (SelectField: DNA, total RNA) 2. Library (SelectField: Fragment, mate-pair) 3. Volume (TextField) 4. Concentration (TextField)
Then in the scv file each row (for a sample) should look like: DNA,Fragment,0.22,24.7
rc
On Mar 23, 2010, at 10:02 AM, nsfox@uwaterloo.ca wrote:
Hi,
What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample?
Thanks, Natalie
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
This error has been fixed in revision 3557. Thanks for reporting this issue. Also, in the csv file the first column should be the sample name. So, in the example I had sent you, it should look like: SampleOne,total RNA,Fragment,0.22,24.7 rc On Mar 23, 2010, at 11:12 AM, nsfox@uwaterloo.ca wrote:
I've attempted this and I'm getting the Error message "Error in importing samples file".
Here's the details of what I did:
My Sequencing sample form specifies on grid level called "Sample Description" with the fields: "Sample Description", "Genus species", and "Comments".
my csv file has only the line of text: Emerging Tassel (Male),Zea mays,test
And all I did to import it is clicked browse within the sequencing request and selected the file, then I pressed import samples. Galaxy navigated back to the Sequencing Request page and there was the Error message in the top right corner and the sample wasn't imported.
Thanks for the help, Natalie
Quoting Ramkrishna Chakrabarty <rc@bx.psu.edu>:
Natalie,
The format of the csv file for importing samples depends on the sample form fields. For example if the sample for fields are: 1. Type (SelectField: DNA, total RNA) 2. Library (SelectField: Fragment, mate-pair) 3. Volume (TextField) 4. Concentration (TextField)
Then in the scv file each row (for a sample) should look like: DNA,Fragment,0.22,24.7
rc
On Mar 23, 2010, at 10:02 AM, nsfox@uwaterloo.ca wrote:
Hi,
What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample?
Thanks, Natalie
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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Ramkrishna Chakrabarty