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Problem with installing SeqPrep from GitHub

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?

seqprep
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updated by Ram Ram • written by jolespin jolespin

1 answer

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.

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written by Alex Reynolds Alex Reynolds

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

git checkout clang-patch
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updated by Ram Ram • written by jolespin jolespin

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.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

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
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updated by Ram Ram • written by u201612208 • u201612208

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

sudo apt-get install zlib1g-dev
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updated by Ram Ram • written by u201612208 • u201612208

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

• 0 views • link
updated by Ram Ram • written by Mitra • Mitra

I think installation by anaconda is easier.

conda install -c bioconda seqprep
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updated by Ram Ram • written by Mitra • Mitra

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