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COMBINE-lab / minnow

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fixfasta executable does not respond appropriately to `--help` or `-h` #9

Closed ghferrari closed 1 year ago

ghferrari commented 4 years ago

I've just attempted to build this on Centos 7.6 with GCC 7.3.0 and the resulting fixfasta executable does not recognise the --help or -h parameters.

hiraksarkar commented 4 years ago

Hi @ghferrari , I hope you are building the refactor branch, which is currently a default, please use the index command to build the index.

ghferrari commented 4 years ago

Sorry, I should have mentioned, this is with release beta_1.5.

hiraksarkar commented 4 years ago

Hi, I would strongly suggest to not use the conda version as of now. They are not letting us use the pre-release, so we are going to go with the full release. Until then please use github repo to build it from source. Let me know if you need the binary.

ghferrari commented 4 years ago

I did indeed build from source using the latest beta_1.5 release available from this page https://github.com/COMBINE-lab/minnow/releases

hiraksarkar commented 4 years ago

Ahh, I see, I should have put a new release, my apologies, can you git pull and build, if it does not work, let me know, I will put the binary here, or issue a release.

hiraksarkar commented 4 years ago

@ghferrari Please try this one https://github.com/COMBINE-lab/minnow/releases/tag/beta_1.6

hiraksarkar commented 4 years ago

After building the version you can build a de-bruijn graph with an oneliner 

src/minnow index -r <fasta.fa> -k 101 -f 20 --tmpdir tmp -p 10 -o <ind_dir>

Here the command line options have the same meaning as described in original twopaco.

ghferrari commented 4 years ago

Hi @hiraksarkar , I tried building beta_1.6 but no fixfasta executable was built - is it supposed to be there or not with this version?

Also, I don't have a fasta.fa file or any other files to test with. Are there some I can download?

hiraksarkar commented 4 years ago

@ghferrari The point of fixfasta was to fix a fasta file (that you want to sequence data from) and then produce a de-bruijn graph from the fasta file that you already have.

The new version does not need those intermediate steps as they would be called internally.

About having the proper fasta file, it is determined by the kind of organism you want your single cell experiment to base on. For example if you work with human, you want to have a human fasta file, which can be downloaded from gencode etc.

ghferrari commented 4 years ago

Thank you, beta_1.6 builds successfully. I will have to ask a colleague to test it with real data.

Many thanks for your help!

hiraksarkar commented 4 years ago

No worries, let me know if you need any help.