How to work with local files with Crossbow ?

[narain]

Dear All

I am using the version 1.2.0 of Crossbow. I have managed to get it working for a file specified in .manifest input file that points to an FTP server.

I am wondering how would you get it to work for a input data that is locally already on your computer, such as .fastq or .fastq.gz file or .sra file ? This will avoid internet dependency.

Also, I tried the bowtie option by specifying the path to bowtie2 and crossbow did not work. Does Crossbow work only for bowtie1 and no other aligner ?

Narain

[9000revs]

Hi Narain:

Can you please provide more details on what version of cluster you made CB work on? If you see my posts, I have been having all kinds of issues with hadoop and CB.

Thanks.

Dear All

I am using the version 1.2.0 of Crossbow. I have managed to get it working for a file specified in .manifest input file that points to an FTP server.

I am wondering how would you get it to work for a input data that is locally already on your computer, such as .fastq or .fastq.gz file or .sra file ? This will avoid internet dependency.

Also, I tried the bowtie option by specifying the path to bowtie2 and crossbow did not work. Does Crossbow work only for bowtie1 and no other aligner ?

Narain

[narain]

@9000revs

I changed the source code at reasonable locations where I thought there are bugs, without changing the actual work flow, and added wrapper simplified execution scripts on top of CrossBow 1.2.0 , and then it works. The modified version is now called HokieCrossBow 1.0 , and has been tested to work fine on HokieSpeed cluster of Virginia Tech. Details of the HokieCrossBow and related tools are at my website in the 'software as service' section www.tinyurl.com/abinarain .

Regards

Narain

[huzefa_mehta]

I am running on Amazon EMR and get Streaming Command Failed!

Can you point me to what you did to resolve the crash?