Problem with installing SeqPrep from GitHub

Question

[jolespin]

I'm trying to install SeqPrep onto my machine but it's not working. I've downloaded it from GitHub and have been following the installation directions on (https://banana-slug.soe.ucsc.edu/bioinformatic_tools:seqprep#installation). When I run the command make, I get the error:

ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SeqPrep] Error 1

Any suggestions on how to fix this error?

Answer 1

[Alex Reynolds]

I submitted a pull request with patches that allowed me to compile SeqPrep under OS X 10.10. If you want to try this out locally, you could do something like:

$ mkdir /tmp/SeqPrep_test
$ cd /tmp/SeqPrep_test
$ git clone https://github.com/alexpreynolds/SeqPrep.git
$ cd SeqPrep
$ git checkout clang-patch
$ make
...

I don't use this tool, so I don't know if my patches yield a binary that generates correct results, but the code compiles.

[jolespin]

I got it to work thank you so much! what is the purpose of this line?

git checkout clang-patch

[Alex Reynolds]

Git lets you keep a history of file changes ("diffs") in different branches. You can switch to different branches in a Git repository to get different sets of patches or features.

I made a fork or copy of the original developer's SeqPrep code repository, and in my fork I set up a branch called clang-patch that contained file changes that allowed SeqPrep to compile. So when you type in git checkout clang-patch, you end up getting the versions of files that contain the changes I made.

[u201612208]

I got the problem like lack of zlib.h.

How can I solve it?

Thank you very much!

cc  -c -Wall -O0 -g -std=c99 SeqPrep.c -o SeqPrep.o
In file included from SeqPrep.c:10:0:
utils.h:7:18: fatal error: zlib.h: There is no file or directory.
compilation terminated.
Makefile:18: recipe for target 'SeqPrep.o' failed
make: *** [SeqPrep.o] Error 1

[u201612208]

Oh I got it! Just write a command like this:

sudo apt-get install zlib1g-dev

[Mitra]

Hi, I tried to use install it same way, but getting error

[[e-mail]1 SeqPrep]$ git checkout clang-patch
error: pathspec 'clang-patch' did not match any file(s) known to git.

Can you please help? Thanks. Mitra

[Mitra]

I think installation by anaconda is easier.

conda install -c bioconda seqprep