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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
16 stars 7 forks source link

An error when installing BamM #44

Open minsookim1983 opened 7 years ago

minsookim1983 commented 7 years ago

Hello,

I am trying to install BamM; however, I got an error. The error message is attached. install error.txt Please, let me know what is wrong with me. Thank you.

Min-Soo

wwood commented 7 years ago

Hi Min-Soo, That's a pain. Can I ask how you downloaded BamM? The recommended way is to use the realeses page https://github.com/Ecogenomics/BamM/releases or better yet, using the version that has been packaged in GNU Guix https://www.gnu.org/software/guix/ . It won't work if you use the "Download zip" on the front GitHub page https://github.com/Ecogenomics/BamM

Hope that helps. ben

minsookim1983 commented 7 years ago

Thank you for your comment. As you response, I downloaded BamM from https://github.com/Ecogenomics/BamM/releases. I think I forget the installation of 'libcfu' and 'htslib'. I installed 'htslib' safely, but not 'libcfu'. First, I can find 'libcfu v0.0.3', not 'v1.0.3', and it is hard to install 'libcfu v0.0.3'. Would you please let me know how to install libcfu safely?

Min-Soo

wwood commented 7 years ago

Both libcfu and htslib are bundled with BamM, so you don't need to worry about those (if you don't want to, htslib can be included as a shared library but it is probably easiest just not to bother). Would you mind sending a log of what is going wrong for you including the commands that you ran please? Thanks, ben

minsookim1983 commented 7 years ago

I am sorry for late answer. Here is the error message I got. Error.txt Thank you.

Min-Soo

hhollandmoritz commented 7 years ago

Hi, I'm getting the same error as Min-Soo after trying the steps above. The only difference is I don't have admin privileges so all of my commands are run without sudo. I was looking through the other threads for hints and so I tried running ./autgen.sh and I get this error:

[hollandh@microbe c]$ ./autogen.sh configure.ac:1: error: m4_defn: undefined macro: _m4_divert_diversion configure.ac:1: the top level autom4te: /usr/bin/m4 failed with exit status: 1 aclocal: autom4te failed with exit status: 1 autoreconf: aclocal failed with exit status: 1

I've tried this on both version 1.7.3 and 1.7.2 in case it was a bug introduced between versions but I get the same error in both. I'm running this code on a RedHat operating system (which I've read is similar to CentOS) which may mean I have the same issues as the user trying to run it on CentOS.

Do you have any suggestions on how to proceed from here? Thanks, Hannah

timbalam commented 7 years ago

I've managed to reproduce a similar error to Hannah's on a CentOS 6 virtual box. We'll try to fix it, however it might take a while. In the meantime, we have recently produced a docker image https://hub.docker.com/r/timbalam/bamm/. If it is possible to use docker on your system, it'd be great to have some people try that. If you do try it, please let us know of any issues using that.

hhollandmoritz commented 7 years ago

Unfortunately, docker is not an option on my system, but I will keep trying to find a work-around as you work on a permanent fix. Thanks so much!

jvollme commented 7 years ago

I think a work-around to this problem was found in #39