*tsv.gz files from /example not downloading correctly

pollicipes commented 6 years ago

Yannick,

The tsv files for doing the example are not downloading correctly, either by cloning the repo or by downloading binless manually. Seeing their size in gitHub says iuts 50 Mb, but when I see it in my folder its only 133 bits, and I am not able to open them from the code in tutorial. This is the error, just in case, but it says that file is empty:

Error in fread(fname, col.names = c("id", "chr1", "begin1", "strand1", : File is empty: /dev/shm/file199ee33727
Traceback:

1. examine_dataset("zcat ~/binless/example/GM12878_MboI_HICall_FOXP1ext.tsv.gz", 
 .     skip = 0L, nrows = 1e+06, skip.fbm = T, read.len = 101)
2. read_tsv(infile, skip = skip, nrows = nrows, locus = locus)
3. fread(fname, col.names = c("id", "chr1", "begin1", "strand1", 
 .     "length1", "re.up1", "re.dn1", "chr2", "begin2", "strand2", 
 .     "length2", "re.up2", "re.dn2"), nrows = nrows, skip = skip)

Thank you!

Best, Juan

pollicipes commented 6 years ago

PS: By downloading manually each of the files separately, seems to work, but I am just informing you about the issue. ;)

J

yannickspill commented 6 years ago

Hi Juan Yes, this is an expected limitation, due to the way how git handles things. These large files you mention are not managed by git itself, but by git lfs. Since it looks like you don't have it installed, you ended up just looking at a symbolic link to the file, not the file itself. So you can

either download the repo manually from the website, as you did
or install git lfs and then checkout the repo using your terminal. Basically this just involves doing brew install git-lfs and then typing git lfs install once (if you are on a mac).

pollicipes commented 6 years ago

Great! Thanks! :D

3DGenomes / binless

*tsv.gz files from /example not downloading correctly #4