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SorenKarst / longread_umi

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Exchange usearch for vsearch #12

Open SorenKarst opened 4 years ago

SorenKarst commented 4 years ago

Anna has shown that usearch can be exchanged for vsearch here #10 . We should make the shift to make installation more smooth and more open.

YulinzhangSia commented 4 years ago

Dear Soren,

Can you show me how to change the usearch path? I have entered the right path when installation, while the pipeline still transfers to the wrong version. I have checked the issue #10, but didn't find the solution. I also looked at the "/scripts/dependencies.sh", while I don't know what should be done.

Thanks Yulin

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SorenKarst commented 4 years ago

Hi Yulin,

You can change the path to usearch manually by editing the "/scripts/dependencies.sh" file. The line that reads "export USEARCH=usearch" should be changed to "export USEARCH=\<path-to-usearch-executable>". If I should do it it would look something like this:: export USEARCH=/scratch/users/smk/software/usearch/usearch11.0.667_i86linux32

All the best Soren

YulinzhangSia commented 4 years ago

Hi Yulin,

You can change the path to usearch manually by editing the "/scripts/dependencies.sh" file. The line that reads "export USEARCH=usearch" should be changed to "export USEARCH=". If I should do it it would look something like this:: export USEARCH=/scratch/users/smk/software/usearch/usearch11.0.667_i86linux32

All the best Soren

Hi Soren,

The problem has been solved, and thank you very much for the attentive reply!

Regards, Yulin

SorenKarst commented 4 years ago

Great!