Closed jlobatop closed 4 years ago
Solved by adding the directory location of the minimap executable to the $PATH
environment variable. One way to do so is by including:
export PATH="${PATH}:~/minimap2"
in the .bashrc
file (replacing ~/minimap2
with your installation folder).
Hi, I downloaded ptolemy.jar, I constructed the file with the list of genomes and annotations but I am running in troubles when executing extract with that list, getting the following output:
I first installed minimap from source, compiling it from GitHub. I verified that minimap2 is working by running the test command of:
./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
which returned the success message. Moreover, I also constructed shell function so minimap2 will point to the compiled file regardless of the folder and I have ensured that I can run it within scripts. As I couldn't make it work, I tried to set the binary file from the releases page of minimap2 in the Ptolemy folder, the folder where I was storing the genomes and the folder I have selected as output, having the same problem again. I also tried to install it from bioconda, again with negative results. I would really appreciate any help anyone can provide in the topic!