Error while installation

[ichauchcc]

Hi team,

Hope you are all well.

Recently we've been trying to install STRetch into HPC system. But it continues to fail. Please see the error message below.

[dleo2939@login3 ~]$
[dleo2939@login3 ~]$  git clone git@github.com:Oshlack/STRetch.git STRetch
Cloning into 'STRetch'...
Warning: Permanently added the RSA host key for IP address '52.64.108.95' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Any suggestion on how we can fix this? Thanks a mil.

CC

[hdashnow]

This looks like a git/GitHub or networking error. You could try cloning via HTTP:
git clone https://github.com/Oshlack/STRetch.git

[ichauchcc]

Thanks for the quick response. It seems like our technician met another problem while downloading, could you please have a look at it?

'''
Unfortunately, both of 2 installations were stuck in the installation phase (mainly, trying to download a huge dataset from the outside world)

See details:

[dleo2939@hpc242 temp]$ cd STRetch/
[dleo2939@hpc242 STRetch]$
[dleo2939@hpc242 STRetch]$ ./install.sh
WARNING: pipelines/pipeline_config.groovy already exists so will be overwritten by this installation. Creating backup pipelines/pipeline_
config.groovy.backup in case you wish to retreive the previous version of this file.
cp: cannot create regular file `/tmp/temp/STRetch/pipelines/pipeline_config.groovy.backup': Permission denied
python not found, fetching it
--2022-06-15 16:43:46-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c84f, ...
Connecting to repo.continuum.io|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [following]
--2022-06-15 16:43:46-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com... 104.16.131.3, 104.16.130.3, 2606:4700::6810:8303, ...
Connecting to repo.anaconda.com|104.16.131.3|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 76607678 (73M) [application/x-sh]
Saving to: “miniconda.sh”

100%[===============================================================================================>] 76,607,678 115M/s in 0.6s

2022-06-15 16:43:47 (115 MB/s) - “miniconda.sh” saved [76607678/76607678]

ERROR: File or directory already exists: '/tmp/temp/STRetch/tools/miniconda'
If you want to update an existing installation, use the -u option.
./install.sh: line 44: /tmp/temp/STRetch/tools/miniconda/bin/conda: No such file or directory
ln: creating symbolic link `/tmp/temp/STRetch/tools/bin/*': File exists
goleft not found, fetching it
./install.sh: line 110: goleft_install: command not found
bedtools not found, fetching it
./install.sh: line 110: bedtools_install: command not found
mosdepth not found, fetching it
./install.sh: line 110: mosdepth_install: command not found
Downloading reference data
--2022-06-15 16:43:47-- https://home.chpc.utah.edu/~u6026198/hg19.STRling.bundle.tar.gz
Resolving home.chpc.utah.edu... 155.101.19.106
Connecting to home.chpc.utah.edu|155.101.19.106|:443... connected.
WARNING: cannot verify home.chpc.utah.edu’s certificate, issued by “/C=US/O=Let's Encrypt/CN=R3”:
Issued certificate has expired.
HTTP request sent, awaiting response... 200 OK
Length: 8788325858 (8.2G) [application/x-gzip]
Saving to: “/tmp/temp/STRetch/reference-data/reference-data.tar.gz”

0% [ ] 2,523,136 317K/s eta 7h 52m ^

'''

Can you please look at the above and share some potential ways to work out the problem? Thank you so much!

Kind regards,

CC

[hdashnow]

You could comment out the line in the install script that downloads the reference data, then download it manually.
Here's the line in the install script:

STRetch/install.sh

Line 127 in dd35b85

download_hg19

And here's the link to download the reference data manually:
https://home.chpc.utah.edu/~u6026198/hg19.STRling.bundle.tar.gz