Fatal error when attempting 'make'

[mshadbolt]

Fatal error when attempting 'make'

[bioinfo-fiend]

I also receive the same issue

[nunofonseca]

Hi,

Did you install the dependencies (zlib and samtools 0.1.9)?

"samtools (version 0.1.19) and zlib (http://zlib.net) version 1.2.11 or latest are required to compile fastq_utils. The install_deps.sh script in the toplevel folder tries to download and compile the dependencies. "

Cheers.

[bioinfo-fiend]

@nunofonseca Do these dependencies need to be located in the same directory? I tried installing these dependencies on my machine and still continued to get this error...

In home directory:

wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -vxjf samtools-1.9.tar.bz2
cd samtools-1.9
make

and similar process for installing Zlib....

[bioinfo-fiend]

@nunofonseca I did a clean install and, installed dependencies samtools and Zlib, still producing same error...

[nunofonseca]

Yes, the Makefile assumes that samtools is installed in the same directory.
You should be able to compile successfully by running the following commands:

./install_deps.sh
make
make install

[bioinfo-fiend]

@nunofonseca

The previous error was not present anymore, I continued to get a secondary error and not able to run the fastq_info command. However, it was just a matter of making the fastq_utils directory executable...

[nunofonseca]

The error seems to be a consequence of a typo: you probably wrote intstall instead of install (make install). The fastq_info and other programs will be copied to the bin/ folder in the toplevel fastq_utils directory.

[bioinfo-fiend]

@nunofonseca thanks for the clarification, everything is working fine. you can close this issue if needed.

[bioinfo-fiend]

@nunofonseca I'm still having issues again, it was working fine yesterday and today when trying to make the fastq_utils directory executable:

e.g.
chmod 700 ./fastq_utils/bin
chmod u+x ./fastq_utils/bin

chmod 700 ./fastq_utils/src
chmod u+x ./fastq_utils/src

-bash-4.2$ export PATH="/home//user/fastq_utils/:$PATH"

[nunofonseca]

Instead of
export PATH="/home//user/fastq_utils/:$PATH"
you may want to do
export PATH="/home//user/fastq_utils/bin/:$PATH"
?
Alternatively, you can simply copy the files in the fastq_utils/bin folder to a folder that is already in the $PATH.

[mshadbolt]

thanks for the debugging, I was successfully able to install now.