Does anybody success to download data using icgc-storage-client ?
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5.7 years ago
sacha ★ 2.1k

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...

icgc download data • 2.5k views
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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 !

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4.4 years ago
morovatunc ▴ 470

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.

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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.

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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.)

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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.

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