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DaehwanKimLab / hisat-genotype

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Allow use alternative location for HISAT2_fnames #5

Closed hsiaoyi0504 closed 3 years ago

hsiaoyi0504 commented 4 years ago

https://github.com/DaehwanKimLab/hisat-genotype/blob/b64186a3a8f92e60f1a7a268190383986b67ad4d/hisatgenotype_modules/hisatgenotype_typing_common.py#L265-L272

Currently, the file location of hisat-genotype is pretty limited. You need to put all the required files in a specific location. Is it possible to update to make all those reference locations flexible and could be fed by command-line arguments?

chbe-helix commented 4 years ago

Hi hsiaoyi,

Thanks for the suggestion! I can add that into the next version of HISAT-genotype coming out soon. For now I suggest using:

ln -s TARGET LINK_NAME

To make a soft links to the files.

hsiaoyi0504 commented 4 years ago

Yes, I use this method. However, it's somewhat dirty and it's not a good practice in terms of an user-friendly tool.

chbe-helix commented 4 years ago

Agreed! I plan to add support for this feature with the new release of HISAT-genotype based in Python 3

hsiaoyi0504 commented 4 years ago

@chbe-helix May I know if this has been resolved by the new 1.3.0 version?

chbe-helix commented 4 years ago

Hi Hsiaoyi,

Short answer is unfortunately no I ran into some time constraints in the conversion. Version 1.3.1 coming in July 2020 will have this feature. Thank you for your continued patience in resolving this issue.

Thanks, Chris

chbe-helix commented 3 years ago

Hi Hsiaoyi,

The new version of HISATgenotype (1.3.1) has been released and has a new option to direct HISATgenotype to an index folder. You should now only have to download the index once and only at install if you desire. The manual will be updated with these changes soon. Thanks!

Thanks, Chris