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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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Is the --sra-acc option available with the binaries? #426

Open scotronq opened 1 year ago

scotronq commented 1 year ago

I downloaded the Intel macos binaries for v2.5.1 (https://github.com/BenLangmead/bowtie2/releases/download/v2.5.1/bowtie2-2.5.1-macos-x86_64.zip) and tried to use the --sra-acc option like below: 

bowtie2 -x  'someIndex' --sra-acc 'SRR000001'  -S  'myFile.sam' --quiet

and got the following error:

"bowtie2-align-s: unrecognized option `--sra-acc' "

The Bowtie2 manual "Building from Source" section states "Prepackaged builds will include a package that supports SRA" and the MANUAL lists "--sra-acc" as an input options. But the bowtie2 help (bowtie2 -h) does not list "--sra-acc" as an option and I got the above error message.

So is the --sra-acc option available with the binaries? Or I am misinterpreting the Manual? (or am I using the option correctly)

Thanks!

ch4rr0 commented 1 year ago

Hello,

I uploaded the SRA package for MacOS x86-64 to GitHub. I will be uploading the remaining packages for Linux and M1 MacOS later today. Thank you for your patience.

scotronq commented 1 year ago

thanks for the quick fix! Could you do this for Windows as well?

ch4rr0 commented 1 year ago

I tried, but was unsuccessful in trying to cross-compile NCBI-VDB. Can you try running the Linux binaries with Windows Subsystem for Linux (WSL)?

P.S. For those waiting on an ARM64 package, v2.10.2 does not have support for ARM. If you are interested in having SRA support I can try putting a package together, but unfortunately cannot include it the current release as that requires a different version of the VDB and NGS libraries.