error when accessing to Umap repository

[Irina Zhegalova]

Hey guys,

Thanks for the great software!

Unfortunately, I cannot access to repository, got a message "We can't let you see this page" is it me or smth wrong?

Thank you in advance

[Mehran Karimzadeh]

Hello Irina,

Bitbucket stopped to support mercurial repositories and we had to move the repository top GitHub: https://github.com/hoffmangroup/umap

We will update the bismap.hoffmanlab.org about this soon.

Thanks,

Mehran

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[Irina Zhegalova]

Hey Mehran,

Thank you!

Btw I've got an issue

in bowtie_to_unique
out_link.write(unique_ar.tobytes())
AttributeError: 'numpy.ndarray' object has no attribute 'tobytes'

Python 3.7.3
numpy 1.19.1

Is it because of python being not 2.7 ?

Thanks!

[Irina Zhegalova]

update: switched to python 2.7, had the same error

[Maciej Jończyk]

I've succeeded installation with git and the site you provided.

What can I do to make umap work on local computer, i.e. without distributing computing?

Now I have following error

"

test_run.sh: 3: test_run.sh: qsub: not found
test_run.sh: 4: test_run.sh: Syntax error: "(" unexpected

[Mehran Karimzadeh]

Hello Maciej,

Any command starting with "qsub" assumes there is an SGE scheduler.

If you want to run umap locally, please consider the following:

1. Remove the qsub-related part of the command

2. Use the -job-id parameter which is designed to allow local run of paralle jobs

example:

in SGE: 

qsub -q hoffmangroup -t 1-3114 -N Bismap.UniqueKmers -terse -tc 120 -hold_jid 1 -cwd -b y -o Bismap.UniqueKmers.LOG -e Bismap.UniqueKmers.ERR python get_kmers.py hg19/chrsize.tsv kmers/k24 k24 chrs -var_id SGE_TASK_ID)

Locally:

for i in {1..3114}

do

    python get_kmers.py hg19/chrsize.tsv kmers/k24 k24 chrs -job-id $i

done

This will of course take long to run for large genomes.

Good luck!

Mehran

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