problem in configuring the genome

[FH96]

Hi everyone,
I'm trying to get started with wgbs_tools but I face this error

[wt init] Setting up genome reference files in /home/fatemeh/wgbs_tools/references/hg19

[wt init] No reference FASTA provided. Attempting to download from
https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz
/bin/sh: 1: curl: not found
Traceback (most recent call last):
File "/home/fatemeh/wgbs_tools/src/python/wgbs_tools.py", line 96, in
main()
File "/home/fatemeh/wgbs_tools/src/python/wgbs_tools.py", line 63, in main
importlib.import_module(args.command).main()
File "/home/fatemeh/wgbs_tools/src/python/init_genome.py", line 297, in main
InitGenome(args).run()
File "/home/fatemeh/wgbs_tools/src/python/init_genome.py", line 57, in init
self.get_fasta()
File "/home/fatemeh/wgbs_tools/src/python/init_genome.py", line 74, in get_fasta
eprint(f'[wt init] Failed downloading reference for genome {self.name}: %d\n%s\n%s' % (p.returncode, output.decode(), error.decode()))
AttributeError: 'NoneType' object has no attribute 'decode

I appreciate any help :)
As I haven't figured the genome, I also face problem doing the tutorial and using convert function:
File "/home/fatemeh/wgbs_tools/src/python/wgbs_tools.py", line 96, in
main()
File "/home/fatemeh/wgbs_tools/src/python/wgbs_tools.py", line 63, in main
importlib.import_module(args.command).main()
File "/home/fatemeh/wgbs_tools/src/python/convert.py", line 305, in main
convert_single_region(args)
File "/home/fatemeh/wgbs_tools/src/python/convert.py", line 285, in convert_single_region
gr = GenomicRegion(args)
File "/home/fatemeh/wgbs_tools/src/python/genomic_region.py", line 28, in init
self.genome_name = get_genome_name(genome_name)
File "/home/fatemeh/wgbs_tools/src/python/genomic_region.py", line 21, in get_genome_name
return os.readlink(refdir)
FileNotFoundError: [Errno 2] No such file or directory: '/home/fatemeh/wgbs_tools/references/default'

[nloyfer]

Hi.
The problem is here:

/bin/sh: 1: curl: not found

Apparently you don't have curl installed.
I updated init_genome.py so it would use wget if curl is not found. Please try again

[FH96]

Thank you for your answer, yes I found out about curl after opening this discussion and installed it. Also, I though curl could be added to the list of dependencies.
By the way, can I ask how much space is required to unzip the hg19 genome?
Thanks again.

[nloyfer]

It takes 3Gb. But in general there is no need to decompress it.
wgbstools init_genome only decompresses it temporarily in order to compress it back in a block-wise manner (using bgzip).
Once the FASTA is bgzip-compressed and indexed one can read chunks from it by running samtools faidx.

[FH96]

Are you sure about 3Gb? I guess it was taking about 20Gb for me and still more space was required...