gmarcais
commented
4 years ago If you installed with conda, then there is nothing else you have to do. After conda install jellyfish, jellyfish should be available to you right away (as long as the proper directory is in your PATH). To check whether that is installed correctly, please ask on a conda list.
The point is you either install it using the source code available on github, or you install it with conda and ignore the instruction on github. What you do above is a mixture of the 2 and will not work.
Let me give you some instructions to compiles and install from source in your HOME directory. Run the following commands:
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz
tar zxf jellyfish-2.3.0.tar.gz
cd jellyfish-2.3.0
./configure --prefix=$HOME
make installAfter that, doing ~/bin/jellyfish --help should get you the help of Jellyfish. (simply jellyfish --help should work as well. If not, check for example https://askubuntu.com/questions/402353/how-to-add-home-username-bin-to-path).
Hope this helps.
Dr-Stef
Hello community! Apologies if the question is silly, I used anaconda with the following command $ conda install jellyfish, then following the GitHub Readme file I tried ./configure, however got the following error:
stefany@ada01:/usr/local$ chos 7 stefany@ada01:/usr/local$ autoreconf -i find:
./share/prank': Permission denied find:./share/bowtie2-2.2.5/example': Permission denied find:./share/bowtie2-2.2.5/doc': Permission denied find:./share/exonerate-2.2.0-x86_64': Permission denied find:./share/consed19/for_itanium': Permission denied find:./var/lib/munge': Permission denied find:./var/log/munge': Permission denied find:./etc/munge': Permission denied ls: cannot access ./acinclude.m4: No such file or directory autom4te: cannot create autom4te.cache: No such file or directory automake: autoconf failed with exit status: 1 stefany@ada01:/usr/local$ cd stefany@ada01:~$ cd /usr/local/ stefany@ada01:/usr/local$ autoreconf -i find:./share/prank': Permission denied find:./share/bowtie2-2.2.5/example': Permission denied find:./share/bowtie2-2.2.5/doc': Permission denied find:./share/exonerate-2.2.0-x86_64': Permission denied find:./share/consed19/for_itanium': Permission denied find:./var/lib/munge': Permission denied find:./var/log/munge': Permission denied find:./etc/munge': Permission denied ls: cannot access ./acinclude.m4: No such file or directory autom4te: cannot create autom4te.cache: No such file or directory automake: autoconf failed with exit status: 1Any idea, recommendation on how to solve this? Thank you!!!