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Question: DiscoSNP INSTALL problem
0
gravatar for dahmani_amel
3.3 years ago by
dahmani_amel • 20
dahmani_amel • 20 wrote:

Hi everybody, I'm trying to install DiscoSNP following this instructions:

-get a local copy of DiscoSnp source code

git clone --recursive https://github.com/GATB/DiscoSnp.git

-compile the code an run a simple test on your computer

cd DiscoSnp

sh INSTALL

But when i try to install it by sh INSTALL, i have this :

INSTALL: 18: INSTALL: cmake: not found
make: *** Pas de cible spécifiée et aucun makefile n'a été trouvé. Arrêt.
Running simple test...
use read set: fof.txt
    Running discoSnp++ 2.2.X, in directory /home/amelmek/DiscoSnp with following parameters:
         read_sets=fof.txt
         prefix=discoRes_k_31_c_auto
         c=auto
         C=2147483647
         k=31
         b=0
         d=1
         D=100
     starting date=jeudi 23 juin 2016, 15:23:28 (UTC+0200)

../run_discoSnp++.sh: ligne 327: /home/amelmek/DiscoSnp/build/bin/read_file_names: Aucun fichier ou dossier de ce type
    ############################################################
    #################### GRAPH CREATION  #######################
    ############################################################
/home/amelmek/DiscoSnp/build/ext/gatb-core/bin/dbgh5 -in fof.txt_discoRes_k_31_c_auto_D_100_P_1_b_0_removemeplease -out discoRes_k_31_c_auto -kmer-size 31 -abundance-min auto -abundance-max 2147483647 -solidity-kind one -mphf none -verbose 0
../run_discoSnp++.sh: ligne 346: /home/amelmek/DiscoSnp/build/ext/gatb-core/bin/dbgh5: Aucun fichier ou dossier de ce type
there was a problem with graph construction
diff: discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa: Aucun fichier ou dossier de ce type
*** Test: FAILURE on diff .fa

Can someone help me please???

Best,

Amel
rna-seq snp discosnp • 1.1k views
ADD COMMENT • link •
modified 3.3 years ago by genomax ♦ 73k • written 3.3 years ago by dahmani_amel • 20
4
gravatar for genomax
3.3 years ago by
genomax ♦ 73k
United States
genomax ♦ 73k wrote:

You need to install cmake for your OS for a start. What OS are you using?
ADD COMMENT • link modified 3.3 years ago • written 3.3 years ago by genomax ♦ 73k

Yes finally i found it out, i didn't read correctly the error message :) i installed cmake on linux and now it works fine!!

THANK YOU :)

ADD REPLY • link written 3.3 years ago by dahmani_amel • 20

Please accept genomax2's answer if it was helpful. Thank you.

Here are the steps to accept an answer, if you need them.

ADD REPLY • link written 3.3 years ago by RamRS ♦ 24k
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