Question: jellyfish v 1.1.11 installation problem
0
gravatar for luyang1005
2.4 years ago by
luyang100520
luyang100520 wrote:

Hi, community,

I run the kraken-build --build --db bacteria It told me I do not have jellyfish version 1. Then I install the jellyfish v1.1.11. Always cannot reach v1, but always reach v2. Since now jellyfish is version2. And since every time I install the jellyfish v1.1.11 source jellyfish-1.1.11.tar.gz, after ./configure, make, make install, it still told me that I installed is jellyfish v2.2.3.

How can I deal with this situation?

Thanks

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ADD COMMENTlink written 2.4 years ago by luyang100520
1
  1. did you uninstall jellyfish v2.2.3?
  2. Is jellyfish v1.1.11 in user path?
  3. Is the command line function different for jellyfish v.2.2.3 and 1.1.11? (for eg jellyfish vs jellyfish_1.1.11)
  4. Probably your default jellyfish command is pointing to jellyfish v2.2.3 instead of v1.1.11. Try uninstalling jellyfish 2.2.3 and reinstall 1.1.11 or use binary direct from installation path.
ADD REPLYlink written 2.4 years ago by cpad011214k

Thanks for the remind. I went back to see, I use the command which -a jellyfish. Then I found the /usr/bin/ has installed the jellyfish version 2.2.3. However, that is the bin, and I do not have the sudo pemission. I just want to install it under my directory. How can I deal with this? Thanks so much.

ADD REPLYlink written 2.4 years ago by luyang100520
1

Make sure the local jellyfish v.1.x directory is in your $PATH before rest of stuff. You can try something like export PATH=/dir_w_local_jellyfish:$PATH and see if that helps.

ADD REPLYlink written 2.4 years ago by genomax90k

Thanks for this info. It works now. Appreciate it!

ADD REPLYlink written 2.4 years ago by luyang100520
1

If you go in the README file in jellyfish, you will read this instructions:

% ./configure --prefix=/my/dir

% make

% make install

You just have to put your home directory (or any desired directory) instead of /my/dir and the software will be installed in that directory.

Then, in that directory, you have to identify the directory in which jellyfish binary is saved and add the folder to your path. This should work. Alternatively, you can ask your sysadmin to install jellyfish 1.1.11

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Fabio Marroni2.6k
2
gravatar for cpad0112
2.4 years ago by
cpad011214k
India
cpad011214k wrote:

Well, you can create a directory (say for eg./home/user/bioinformatics_progs/bin) and keep jellyfish binary. Add that to your path. In bash, it is .bashrc or .bash_profile.

$ mkdir /home/user/bioinformatics
$ tar xvzf tar jellyfish-1.1.11.tar.gz --directory=/home/user/bioinformatics/ (from location of tar.gz)
$ cd /home/user/bioinformatics/jellyfish-1.1.11/
$ ./configure --prefix=/home/user/bioinformatics/jellyfish-1.1.11
$ make
$ make install
$ cd bin # (if installation is successful, you should see a directory bin and in side bin directory you should see jellyfish executatble)
$ pwd #prints the current directory of jellyfish binary

open .bashrc (located in your home directory), add export path=$PATH:/home/user/bioinformatics/jellyfish-1.1.11/bin:

then do . .bashrc. Jellyfish1.1.1 should be availabe to you now.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by cpad011214k

That's what I was trying to suggest, but you did by far a better job!

ADD REPLYlink written 2.4 years ago by Fabio Marroni2.6k

It works now!! Really helpful!!

ADD REPLYlink written 2.4 years ago by luyang100520
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