Question: Does anybody success to download data using icgc-storage-client ?
0
gravatar for sacha
3.1 years ago by
sacha1.7k
France
sacha1.7k wrote:

I'm trying to download data from the excellent icgc portal.

I have a DACO account, and I have my access token generate from icgc portal. I download icgc-storage-client, set the config file with my access token.

Now, when I try to download file, using the following command :

icgc-storage-client download --object-id 0429f668-437b-5943-8e32-6ba1743628ed --output-dir /tmp

I get nothing ! And using the url by the following command :

URL=`icgc-storage-client url --object-id 0429f668-437b-5943-8e32-6ba1743628ed`

wget $URL

I get an access denied! I may miss something in the process . Do you know what is it ? From the documentation, it says something about "creating a computer instance to run icgc-storage-client", I don't understand what the purpose...

download icgc data • 1.6k views
ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.1 years ago by sacha1.7k

hello! glad to see it! Now, I come up with the same problem,have you solve it?and how did you solve it? Appreciated to hear from you !

ADD REPLYlink written 22 months ago by Bruce0
1
gravatar for morovatunc
22 months ago by
morovatunc400
Turkey
morovatunc400 wrote:

I have faced with the same problem before. I tried to download icgc data to my local from my local machine. Because all the data is stored in the amazon AWS cloud and you need to log-in to the AWS. Create an instance ( like a cloud machine ) and download icgc client overthere. Later on, you can use icgc client like you have attempted before.

HTH,

T.

ADD COMMENTlink modified 22 months ago • written 22 months ago by morovatunc400

Hi morovatunc,

I have Create an instance in amazon ec2 and log-in it, also installed the icgc client in the ec2, but when I try to use icgc-storage-client to download the data from aws, it still give errors:

icgc-storage-client --profile aws download --object-id am9133b9-6763-5d75-b11b-c93f0b0c9122 --output-dir data
ERROR: Command error: java.io.IOException: Access refused by repository. Ensure client is running as part of repository cloud.                                                                  

Please check the log for detailed error messages

I have log in ec2 cloud, why it still reports 'Ensure client is running as part of repository cloud.' ? Could you give more details for download icgc data from amazon cloud? Thanks so much.

ADD REPLYlink modified 5 months ago by RamRS20k • written 10 months ago by summer00710

I think you should write to ICGC help desk. They are very helpful.

Also I suggest you to log in to the spesific ec2 region. As far as I know, USA ec2 servers have access to icgc data. Final thing, make sure you set your key code. (The code that lets you access to the restricted data.)

ADD REPLYlink written 10 months ago by morovatunc400

Thanks so much.

I log in US East (Ohio) region EC2, I have DACO Cloud Access now, so I have the accessToken and have set it in icgc-storage-client-1.0.23/conf/application.properties file.

I will write to ICGC help desk. Thanks.

ADD REPLYlink modified 5 months ago by RamRS20k • written 10 months ago by summer00710
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