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Installation issues #908
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Update. My boss (who has root access) was able to help me get around the second issue by adding a |
@afkoeppel you could use conda to install gemini. See here: https://bioconda.github.io/recipes/gemini/README.html This works for us quite well. |
conda is not working well in all cases:
Is this a 2!=3 issue? |
I would follow the installation instructions here: |
This is for student training machines which have a variety of software installed so I'm avoiding potential for machine breakage. I've gone with a docker image. |
OK. We are moving to this: https://github.com/brentp/slivar |
Thanks. I'll look into it. |
Hello! I am very excited to use Gemini in my current research project. I am trying to install Gemini on my Macbook and I run into the following error. All requested packages already installed. /Users/aleks/geminiStuff/data/anaconda/bin/gemini --annotation-dir /Users/aleks/geminiStuff/data/gemini_data update --dataonly --tooldir /Users/aleks/geminiStuff/tools I am confused as to what is happening as I created two new directories for the tools and data. I am using the automated gemini_install.py script. I am pretty novice when it comes to commandline tools. My command that produced the above error was: python gemini_install.py ~/geminiStuff/tools ~/geminiStuff/data I am currenlty trying to install this using a Python 2.7 conda environment. If someone could point me in the right direction as to what I'm doing wrong that would be amazing. |
I'm unable to install gemini on our linux server and was hoping for some assistance. I'm using a GNU/Linux server, on which I do not have sudo permission.
I first tried using the recommended installation script:
wget https://github.com/arq5x/gemini/raw/master/gemini/scripts/gemini_install.py
python gemini_install.py ~gemini ~gemini
It seems to install most of the packages, but then dies with:
Traceback (most recent call last): File "gemini_install.py", line 191, in <module> main(parser.parse_args()) File "gemini_install.py", line 84, in main install_rest(gemini, args) File "gemini_install.py", line 149, in install_rest subprocess.check_call(cmd) OSError: [Errno 2] No such file or directory
I then attempted to install it directly using conda:
conda install -c bioconda gemini
This installation appeared to work fine, but none of the annotation files were installed, and when I tried to install them with (e.g.):
gemini update --dataonly --extra gerp_bp
I got a permission error:OSError: [Errno 13] Permission denied: '/.automount'
Apologies if this problem already has a posted answer, or if I'm doing something stupid. None of the other threads I looked at showed this exact problem. I'm guessing it has something to do with file permissions on my server, but I'm able to write most places other than root. I don't know what '/.automount' is or why it's trying to write there.
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