search

NCIP / cgr-bambino

Bambino: SNP caller and Alignment Viewer for Next Gen Data
https://cgwb.nci.nih.gov/cgi-bin/bambino
Other
3 stars 1 forks source link

Connection to the download and website times out #2

Open amanjeev opened 8 years ago

amanjeev commented 8 years ago

Hello, I am trying to visit https://cgwb.nci.nih.gov/cgi-bin/bambino but the connection times out. I am also trying to download the jar via the following and the connection times out there as well.

curl -o bambino.jar -OL https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle

I am not sure if the URL etc. have changed. Can anyone point me to the right direction?

Thanks.

finneyr commented 8 years ago

I'm not sure what's up.

I'll have a look at it and get back with you.

What do you want to use bambino for? Note that we now have Alview for https://github.com/NCIP/alview viewing bam files.

Contact me at finneyr@mail.nih.gov and I can email you the jar file.

From: Amanjeev Sethi [notifications@github.com] Sent: Thursday, November 05, 2015 10:29 PM To: NCIP/cgr-bambino Subject: [cgr-bambino] Connection to the download and website times out (#2)

Hello, I am trying to visit https://cgwb.nci.nih.gov/cgi-bin/bambino but the connection times out. I am also trying to download the jar via the following and the connection times out there as well.

curl -o bambino.jar -OL https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle

I am not sure if the URL etc. have changed. Can anyone point me to the right direction?

Thanks.

— Reply to this email directly or view it on GitHubhttps://github.com/NCIP/cgr-bambino/issues/2.

amanjeev commented 8 years ago

@finneyr Thanks for your response. I need bambino to run this https://github.com/DCGenomics/hackathon_v001_rnaseq (which was a pipeline written by someone else). Thanks for pointing me to https://github.com/NCIP/alview.

As a backup measure, would you mind release the jar here, in your Github repo as well? I believe, you can can attach a binary release on Github.

finneyr commented 8 years ago

Clarification: bambino site for documentation and jar files is temporarily not available. There's not a firm time for getting that back up; but we are working on it. Meanwhile ; I've put a file called "bambino_jars.tar" on this github site which contains the jars and documentation. Please contact me at finneyr@mail.nih.gov if you need anything else. Alview is a new, easier to use tool for viewing bam files. It does not do mass SNP calling (though it will output ATCGInsDel counts for a location).

amanjeev commented 8 years ago

Thanks a lot @finneyr. You can attach release binaries to Github and give the release URL instead of checking in the jars.tar. Please see: https://github.com/blog/1547-release-your-software

That will save you some emails. :-)