This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Mina recompile for larger kmer error

I have been trying to recompile minia to run on a larger kmer length with the following command from the manual

`make clean && make k=100

but I receive the error

make: *** No rule to make target 'clean'. Stop.

typing make produces the error:

make: *** No targets specified and no makefile found. Stop.

So it appears minia does not have a makefile? I've tried reinstalling it and that does not solve the issue. Is there a way other than 'make' to recompile for a larger kmer? Or is there some other solution or mistake I am making?

thank you, any and all help appreciated.

minia kmer recompile
• 1,917 views • link
written by JackyBurton • JackyBurton

Are you using these commands in the source code folder for Minia?

If you are using Minia on a shared machine/server then you would not be able to do this for the application installed for common use. You would need to compile your own copy with larger kmer from source.

• 1 views • link
written by GenoMax GenoMax

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Optimizing the parameters k in Abyss
    written by Maliha • Maliha
    I want to do genome assembly of chicken. I am trying to optimize the kmer value for AByss using this [tutorial][1] and code - #!/bin/bash …
  • velvet adjust MAXKMERLEGNTH on HPC
    written by rrsowmya • rrsowmya
    I am using velvet assembler on the HPC which comes with a default maxkerlength of 31. How should I change this to a higher value? …
  • soapdenovo2 install on UBUNTU 18.04LTS
    written by choi.yisoo.hi • choi.yisoo.hi
    Hello, is there anyone who install soapdenovo2 on UBUNTU18.04? I want to use this program, but I cannot make this source. I downloaded it from …
  • Cufflinks installation error
    written by saj98 saj98
    Hello everyone I am trying to install cufflinks using the following command `/build_dir/cufflinks-2.2.1.Linux_x86_64$ configure --prefix=/usr/bin/samtools/to/cufflinks/install --with-boost=/usr/bin/to/boost --with-eigen=/home/shaima/build_dir/to/eigen` then it run fine with no error, so …
  • problem in installing R
    written by majeedaasim • majeedaasim
    I unpacked the R tar file and configured it successfully in ubunto. Now when I typed "make" following error appears cup-ProLiant-ML150-Gen9% make make: *** No …
  • Error to install GMAP 2017
    written by irving.jgalo23 • irving.jgalo23
    Hi guys **Can you help me?, im trying to install GMAP, the latest version, but when Im compiling the program with the 'make' command, i …
  • vcftools tools install on ubuntu 14.04
    written by bioguy24 bioguy24
    <p>I an installing vcftools from github and have two questions:</p> <p>1. where do I put the samtools1.2 folder so that the tabix and bgzip index …
  • DiscoSNP++ compilation problem
    written by tkitapci tkitapci
    Hi, I am getting this error: ``` bash-4.1$ ./compile_discoSnp++.sh Compiling discoSnp, from directory /home/cmb-02/sn1/tkitapci/software/DiscoSNP++-2.2.0-Darwin mkdir: cannot create directory `build': File exists CMake Error at CMakeLists.txt:25 …
  • kmergenie - Error 1 - It is doesnt work when I typed 'make'
    written by margxenscienculo margxenscienculo
    Good morning. I am trying to use kmergenie v1.6972. But it is broken when I typed "make" ``` sudo make g++ -o minia/Pool.o -c minia/Pool.cpp …
  • bowtie2 installation unsuccessful
    written by bigbang • bigbang
    I have a MAC OS 10.7.5. I just downloaded the latest version of bowtie2: bowtie2-2.2.4 and wanted to install it. After I unzipped the file …