STRetch
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Oshlack
Error while installation
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 [email protected]: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
This looks like a git/GitHub or networking error. You could try cloning via HTTP:
git clone https://github.com/Oshlack/STRetch.git
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
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: https://github.com/Oshlack/STRetch/blob/dd35b85e3bd0f6c58f6e76ec9e5a47ab0e98987c/install.sh#L127
And here's the link to download the reference data manually: https://home.chpc.utah.edu/~u6026198/hg19.STRling.bundle.tar.gz