#125 crossbow manifest file format

[darked90]

I am trying to run simple crossbow example on a local computer, so far
with some problems.

$CROSSBOW_HOME/cb_local --input=small.manifest --preprocess
--reference=$CROSSBOW_REFS/e_coli --output=output_small
--all-haploids --cpus=1

If possible, I would like to skip downloading fairly large
SRR014475.lite.sra file from NCBI using ftp each time I am trying to
run the script. Since I already have file on my computer (I compared
the sizes and md5sum with SRR014475.lite.sra
downloaded with Aspera client) I wan to give a local file as an input
using small.manifest .
Problem is neither of these workd
file://localhost/path/2/SRR014475.lite.sra
/path/2/SRR014475.lite.sra

Can you kindly help me with that one?

Also for the next update, if possible can you simply put commented out
lines as examples how the each of the options should look like:
(from http://bowtie-bio.sourceforge.net/crossbow/manual.shtml#manifest-files\)
On the local computer
In HDFS
In S3
On an FTP or web server

That will really help the beginners, I think.

Best wishes

Darek Kedra,