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kingsfordgroup / armatus

BSD 2-Clause "Simplified" License
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how to run Armatus using hic file as input #16

Open jiangshan529 opened 1 year ago

jiangshan529 commented 1 year ago

Hi, dear all,

I am new to use Armutas. I am wondering how to run Armatus using hic file as input. Thanks!

yihangs commented 1 year ago

Hi,

Thank you for your interest. You can read the Armatus README file from GitHub as the starting point, it tells you how to run Armatus from several kinds of hic input files. Feel free to contact us if you have further questions.

jiangshan529 commented 1 year ago

Hi,

Thank you for your interest. You can read the Armatus README file from GitHub as the starting point, it tells you how to run Armatus from several kinds of hic input files. Feel free to contact us if you have further questions.

Hi, Yihang,

Thanks for your reply. Now I have two questions:

  1. I downloaded the ubuntu version of Armatus as shown below. When I run it on Linux, it said "armatus: command not found". Does it mean I must install Armatus from source? 
    ~/hic/armatus_ubuntu/Armatus-latest_ubuntu-12.04/bin$ ll
total 3880
drwxrwxr-x 2 jib79 jib79    4096 Sep  1  2017 ./
drwxrwxr-x 4 jib79 jib79    4096 Sep  1  2017 ../
-rwxrwxr-x 1 jib79 jib79 3964832 Sep  1  2017 armatus*
jib79@shosty:~/hic/armatus_ubuntu/Armatus-latest_ubuntu-12.04/bin$ armatus
armatus: command not found
  2. for the input file with -S option, now I have a three column sparse matrix file on chr19 like this, is this ok as an input file for Armatus? 60000 65000 1 60000 70000 1 60000 85000 1 85000 85000 26 85000 90000 16 90000 90000 53 90000 95000 12 95000 95000 27 85000 100000 1 90000 100000 2 95000 100000 10 100000 100000 20 95000 105000 1 100000 105000 14

Thanks!

yihangs commented 1 year ago

For the first question: You can download via git clone https://github.com/kingsfordgroup/armatus.git and go to the directory ./armatus/binaries to see if you can directly run those executive files, otherwise you may need to compile it by yourself. For the second question, For the first two columns, you need to divide them by the resolution. Hope it helps.

jiangshan529 commented 1 year ago

Hi, Yihang,

I cloned the git and in the /armatus/binaries directory there are three files:

armatus-linux-x64 armatus-v2.3-macos-10.12 armatus-v2.3-ubuntu-x86_64

I just run the file name in linux like this 'armatus-linux-x64', it said "armatus-linux-x64: command not found". Am I using that correctly?

Thanks

yihangs commented 1 year ago

try to use ./armatus-linux-x64 instead of armatus-linux-x64

jiangshan529 commented 1 year ago

try to use ./armatus-linux-x64 instead of armatus-linux-x64

Hi, Yihang,

When I run it, it said "./armatus-linux-x64: error while loading shared libraries: libboost_iostreams.so.1.55.0: cannot open shared object file: No such file or directory". It seems to be Boost problem, I have installed Boost followed this link: https://www.linuxfromscratch.org/blfs/view/7.5/general/boost.html. But the installation is not successful since I am not the sudo user. Do you have any idea to install this?

Thanks.

yihangs commented 1 year ago

Yeah installing the libraries is always annoying. I think the best way is to contact the person that helps maintain your cluster to see if he/she can help.