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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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CNVnatorv0.3.2, root 6.04.10, Ubuntu 14.04, and make #13

Closed zinj97 closed 8 years ago

zinj97 commented 8 years ago

I have successfully installed root version 6.04.10, and I have installed the CNVnator version of samtools but when I go to compile the CNVnator code with make I keep getting the following error. The version of Ubuntu is running BioLinux

Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.3.2\" -fopenmp -I/include -Isamtools -Isamtools/htslib-1.2.1 -c cnvnator.cpp -o obj/cnvnator.o In file included from cnvnator.cpp:14:0: HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory

include 

                ^

compilation terminated. make: *\ [obj/cnvnator.o] Error 1

I get the same with make OMP=no

I realize that this was previously been associated with ROOTSYS and the LD_LIBRARY_PATH settings but even when these are correct I get the same error.

The .TFrame.h is in the correct setting for root in /data/software/root-6.04.10/graf2d/graf/inc

set command provides the following (partial output)

GID=1014 GNOME_KEYRING_CONTROL=/run/user/1002/keyring-xVuzel GNOME_KEYRING_PID=119570 GPG_AGENT_INFO=/run/user/1002/keyring-xVuzel/gpg:0:1 GTK_IM_MODULE=ibus GTK_MODULES=overlay-scrollbar HISTCHARS='!^#' HISTCMD=723 HISTFILE=/home/philbup/.zsh_history HISTSIZE=2000 HOME=/home/philbup HOST=MDHS-NIX-028 IFS=' ' KEYBOARD_HACK='' KEYTIMEOUT=40 LANG=en_AU.UTF-8 LANGUAGE=en_AU:en LD_LIBRARY_PATH=/data/software/root-6.04.10/lib LIBPATH=/data/software/root-6.04.10/lib LINENO=377 LINES=51 LISTMAX=100 LOGCHECK=60 LOGNAME=philbup MACHTYPE=x86_64 MAIL=/var/mail/philbup MAILCHECK=60 MAILPATH='' MANPATH=/data/software/root-6.04.10/man/man1:/man1:/man1:/man1:/data/software/root/man:/usr/local/man:/usr/local/share/man:/usr/share/man MATE_DESKTOP_SESSION_ID=this-is-deprecated MODULE_PATH=/usr/lib/x86_64-linux-gnu/zsh/5.0.2 NULLCMD=cat

Do I need to change something in the Makefile? or could be problem with the .Zsh shell?

abyzov commented 8 years ago

Hello, sorry for late reply. I think you need to set shell ROOTSYS variable to the location where ROOT is installed. For example

echo $ROOTSYS /Users/abyzov/bin/root-6.04.02

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research,

Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Dec 14, 2015, at 1:51 AM, zinj97 notifications@github.com<mailto:notifications@github.com> wrote:

I have successfully installed root version 60410, and I have installed the CNVnator version of samtools but when I go to compile the CNVnator code with make I keep getting the following error The version of Ubuntu is running BioLinux

Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v032\" -fopenmp -I/include -Isamtools -Isamtools/htslib-121 -c cnvnatorcpp -o obj/cnvnatoro In file included from cnvnatorcpp:14:0: HisMakerhh:11:20: fatal error: TFrameh: No such file or directory

include

^ compilation terminated make: *\ [obj/cnvnatoro] Error 1

I get the same with make OMP=no

I realize that this was previously been associated with ROOTSYS and the LD_LIBRARY_PATH settings but even when these are correct I get the same error

The TFrameh is in the correct setting for root in /data/software/root-60410/graf2d/graf/inc

set command provides the following (partial output)

GID=1014 GNOME_KEYRING_CONTROL=/run/user/1002/keyring-xVuzel GNOME_KEYRING_PID=119570 GPG_AGENT_INFO=/run/user/1002/keyring-xVuzel/gpg:0:1 GTK_IM_MODULE=ibus GTK_MODULES=overlay-scrollbar HISTCHARS='!^#' HISTCMD=723 HISTFILE=/home/philbup/zsh_history HISTSIZE=2000 HOME=/home/philbup HOST=MDHS-NIX-028 IFS=' ' KEYBOARD_HACK='' KEYTIMEOUT=40 LANG=en_AUUTF-8 LANGUAGE=en_AU:en LD_LIBRARY_PATH=/data/software/root-60410/lib LIBPATH=/data/software/root-60410/lib LINENO=377 LINES=51 LISTMAX=100 LOGCHECK=60 LOGNAME=philbup MACHTYPE=x86_64 MAIL=/var/mail/philbup MAILCHECK=60 MAILPATH='' MANPATH=/data/software/root-60410/man/man1:/man1:/man1:/man1:/data/software/root/man:/usr/local/man:/usr/local/share/man:/usr/share/man MATE_DESKTOP_SESSION_ID=this-is-deprecated MODULE_PATH=/usr/lib/x86_64-linux-gnu/zsh/502 NULLCMD=cat

Do I need to change something in the Makefile? or could be problem with the Zsh shell?

— Reply to this email directly or view it on GitHubhttps://github.com/abyzovlab/CNVnator/issues/13.