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stevemussmann / BayesAss3-SNPs

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
GNU General Public License v3.0
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Installation problems (docker) #15

Closed quinn-ca closed 1 year ago

quinn-ca commented 1 year ago

Hello,

I'm looking forward to running this software, however, I'm having difficulty with the installation. I'm installing via Docker to ensure I have all the dependencies, and this is my first time using this program. Everything seems to have gone correctly, using pull to install, then executing runDocker.sh. This does indeed create a data folder.

However, I'm confused about the line in the ReadMe, "In addition to BA3-SNPs, the countLociImmanc.sh script, BA3-SNPS-autotune, and file conversion scripts (stacksStr2Immanc.pl and pyradStr2Immanc.pl) are also installed in your $PATH in this container." I don't see these scripts in the 'data' folder where I executed runDocker.sh, or the /apps/data folder. If they are installed elsewhere, they don't seem to be accessible on my path. I ran /countLociImmanc.sh -f autosomal_genstr_filtered_maxMeanDP49_rmRelated.immanc from both data folders mentioned above and got the error:

./countLociImmanc.sh: No such file or directory

Should I be installing these scripts separately? I thought these would be installed using Docker, but I'm new to this method for installing programs. I sincerely appreciate any help you can provide!

Quinn

stevemussmann commented 1 year ago

Hi Quinn,

You should be able to run the script in the Docker container without specifying the script's location. In other words, you should be able to run countLociImmanc.sh -f autosomal_genstr_filtered_maxMeanDP49_rmRelated.immanc without specifying ./ in front of the script name.

quinn-ca commented 1 year ago

Thank you! What a refreshingly straightforward fix; it worked and returned the expected number of loci.

Cheers, Quinn