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Question: Problem with installing SeqPrep from GitHub
0
Entering edit mode
4.8 years ago
jolespin • 120
United States

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?

ADD COMMENTlink 4.8 years ago jolespin • 120 • updated 4.8 years ago Alex Reynolds 28k
4
Entering edit mode
4.8 years ago
Alex Reynolds 28k
Seattle, WA USA

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.

ADD COMMENTlink 4.8 years ago Alex Reynolds 28k
Entering edit mode
0

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

git checkout clang-patch
ADD REPLYlink 4.8 years ago
jolespin
• 120
Entering edit mode
0

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.

ADD REPLYlink 4.8 years ago
Alex Reynolds
28k
Entering edit mode
0

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

ADD REPLYlink 2.2 years ago
u201612208
• 0
Entering edit mode
0

oh i got it! just write a command like this:

sudo apt-get install zlib1g-dev

ADD REPLYlink 2.2 years ago
u201612208
• 0
Entering edit mode
0

Hi, I tried to use install it same way... but getting error [medsmit@login2.marc1 SeqPrep]$ git checkout clang-patch error: pathspec 'clang-patch' did not match any file(s) known to git.

Can you please help? Thanks. Mitra

ADD REPLYlink 2.1 years ago
Mitra
• 0
Entering edit mode
0

I think installation by anaconda is easier. conda install -c bioconda seqprep

ADD REPLYlink 2.1 years ago
Mitra
• 0

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