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BoevaLab / SV-Bay

Detection of structural variants in cancer mate-pair and paired-end data
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Links given on README file under data folder are no longer active #1

Closed nvarghese closed 7 years ago

nvarghese commented 8 years ago

Links given on README within data folder no longer work.Are the files removed?Are they avaialble elsewhere?

vbaillet commented 8 years ago

Hi, The links provided to download the test data (bam, gem & fasta files) are still dead despite the recent update of data/readme... Would it be possible to update these as well? I indeed get some errors while running SV-Bay on my own data, therefore I'd be glad to know if this has to do with formatting issues on my side. Thanks, Victoire

dashainparis commented 8 years ago

Hi Victoire,

did it work on test data?

We are rewriting readme file - will be ready by the end of the week.

What errors do you have on your data? And on which step?

Daria

2016-03-13 16:38 GMT+03:00 vbaillet notifications@github.com:

Hi, The links provided to download the test data (bam, gem & fasta files) are still dead despite the recent update of data/readme... Would it be possible to update these as well? I indeed get some errors while running SV-Bay on my own data, therefore I'd be glad to know if this has to do with formatting issues on my side. Thanks, Victoire

— Reply to this email directly or view it on GitHub https://github.com/InstitutCurie/SV-Bay/issues/1#issuecomment-195959042.

Best regards,

Iakovishina Daria

dashainparis commented 8 years ago

Hi Victoire,

all bright new readme is ready!

Daria

2016-03-16 22:08 GMT+03:00 Daria Iakovishina yakovishinad@gmail.com:

Hi Victoire,

did it work on test data?

We are rewriting readme file - will be ready by the end of the week.

What errors do you have on your data? And on which step?

Daria

2016-03-13 16:38 GMT+03:00 vbaillet notifications@github.com:

Hi, The links provided to download the test data (bam, gem & fasta files) are still dead despite the recent update of data/readme... Would it be possible to update these as well? I indeed get some errors while running SV-Bay on my own data, therefore I'd be glad to know if this has to do with formatting issues on my side. Thanks, Victoire

— Reply to this email directly or view it on GitHub https://github.com/InstitutCurie/SV-Bay/issues/1#issuecomment-195959042 .

Best regards,

Iakovishina Daria

Best regards,

Iakovishina Daria

dashainparis commented 8 years ago

All bright new readme is awaiting for you on github!

Отправлено с iPhone

15 февр. 2016 г., в 20:54, nvarghese notifications@github.com написал(а):

Links given on README within data folder no longer work.Are the files removed?Are they avaialble elsewhere?

— Reply to this email directly or view it on GitHub.

dashainparis commented 8 years ago

Sorry, I will change it asap,and will send you a new link.

2016-08-10 11:50 GMT+03:00 deloger notifications@github.com:

Hi, the dropbox link to download test bam file is broken, here below the message from dropbox : "Ce fichier ne se trouve plus ici. Quelqu'un a peut-être supprimé le fichier ou désactivé le lien."

Best regards

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/InstitutCurie/SV-Bay/issues/1#issuecomment-238804626, or mute the thread https://github.com/notifications/unsubscribe-auth/AC4R6sxdiUHLnDFY6Ti7FuQ941-psqqoks5qeZDCgaJpZM4Haitn .

Best Regards,

Iakovishina Daria, Ph.D CEO Ksivalue.com tel: +79160881307

zhanghappy123 commented 7 years ago

Hi I'm having issues getting the first step main_clustering.py) to run. In the log file,it is complaining follow: Traceback (most recent call last): File "~/SV-Bay/src/main_clustering.py", line 89, in Process(data_file, config) File "~/SV-Bay/src/main_clustering.py", line 67, in Process cf.CollectStats() File "~/SV-Bay/src/chrfragments.py", line 58, in CollectStats
self.chr = self.rf[0].first_read_chr IndexError: list index out of range

anyone tell me how to solve it ? thanks

zhanghappy123 commented 7 years ago

Hi,dashainparis: The links(https://github.com/InstitutCurie/SV-Bay) provided to download the test data (bam, gem & fasta files) are still dead. can you give me all test data in this mailbox reply or give me a link to download? I indeed get some errors while running SV-Bay on my own data, therefore I'd be glad to know if this has to do with formatting issues on my side. thanks

dashainparis commented 7 years ago

Hello everyone, I've changed the links for the test data. Thank you for patience. Please also update the code, I added some changes on it.