pipeline installation fails

[kamalfartiyal84]

I am running the following command:

snakemake --use-conda -p all

The log file of the error attached herewith.

2019-08-27T144630.839988.snakemake.log

[jagos01]

I am having the same issue. I have tried the standard and alternative methods of installation and both fail with an error in rule map_minimap2

2019-08-27T130612.565348.snakemake.log

[cdg021527]

Hi,

I am having the same issue where installation fails when it tries to install minimap2. Does anyone have any suggestions, or know if any progress has been made to fix this problem?

[ttbond]

The same problem too.

[cluhaowie]

same problem too.

[BCArg]

Same here, I have tried few things, some of which worked partially, as described here

[BCArg]

I have found the same pipeline from nanopore, though hosted elsewhere that works on their sample data set.

Here's the link to the github page

[LotusWang0723]

I came across this problem too, I solved this problem by running the command with just 1 thread like:
$ snakemake --snakefile ./pipeline-structural-variation/Snakefile --configfile ./config.yaml --jobs 1 eval
(I found there were 4 separated bam file in /Analysis/alignments/ which should be concatenated into 1 bam file)

(btw, I am not a developer of this project)

good luck