Install augustus from source without root privileges #358
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Thank you! This worked for me and saved me hours of pain. If our paths ever cross, I owe you a beer. |
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Hi, thanks for this, super useful! :) I followed all your instructions but I got an error on: I do not have libboost_iostreams.so.1.71.0, I have these instead: any advice on how to fix this? |
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You could try a softlink with the required file name. However, it might
produce a segmentation fault. But it’s worth a try.
AnneJRomero ***@***.***> schrieb am Do. 8. Sept. 2022 um
10:48:
… Hi, thanks for this, super useful! :)
I followed all your instructions but I got an error on:
$ augustus --version
augustus: error while loading shared libraries:
libboost_iostreams.so.1.71.0: cannot open shared object file: No such file
or directory
I do not have libboost_iostreams.so.1.71.0, I have these instead:
$ ls libboost_iostreams.*
libboost_iostreams.a libboost_iostreams.so.1.73
libboost_iostreams.so libboost_iostreams.so.1.73.0
libboost_iostreams.so.1
any advice on how to fix this?
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Hi, I tried that and I'm still getting the same error message. |
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That’s weird. If the links are in the correct place, C++ programs usually
try to use the files.
AnneJRomero ***@***.***> schrieb am Do. 8. Sept. 2022 um
11:13:
… You could try a softlink with the required file name. However, it might
produce a segmentation fault. But it’s worth a try. AnneJRomero *@*.
*> schrieb am Do. 8. Sept. 2022 um 10:48: … <#m_-7890995221488165899_> Hi,
thanks for this, super useful! :) I followed all your instructions but I
got an error on: $ augustus --version augustus: error while loading shared
libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No
such file or directory I do not have libboost_iostreams.so.1.71.0, I have
these instead: $ ls libboost_iostreams. libboost_iostreams.a
libboost_iostreams.so.1.73 libboost_iostreams.so
libboost_iostreams.so.1.73.0 libboost_iostreams.so.1 any advice on how to
fix this? — Reply to this email directly, view it on GitHub <#358 (comment)
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Hi, I tried that and I'm still getting the same error message.
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Hi, I'm retrying again. For the step, 'Compile augustus and the auxiliary programs': make MYSQL=false augustus auxprogs I get the error: mkdir -p bin What am I doing wrong? |
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@AnneJRomero Can you start from a fresh conda environment, show the commands you execute with their output? If it helps, on my setup and this is my conda environment: |
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Hi, I copied your list of packages, installed ones that I didn't have and updated the packages that were outdated. I'm not getting the error message anymore. : Thank you! :) I tried testing the installation with: Why am I getting 'Segmentation fault (core dumped)' error? |
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I had the same problem as AnneJRomero. For some reason I couldn't install the same package versions as listed by dario using conda. |
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We have several docker containers that have Augustus with all dependencies. For example, it's in the GALBA container (https://github.com/Gaius-Augustus/GALBA). These containers can be executed either with Docker, or Singularity (the latter for non-root scenarios). |
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I had the same problem as AnneJRomero. ( ´•̥̥̥ω•̥̥̥` ) |
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g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc |
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It exceeds my patience to compile AUGUSTUS without root permissions on our
HPC. We have instructions, see
https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md ,
where also Troubleshooting sections are linked. I recommend running the
Docker container in Singularity.
…On Thu, Mar 14, 2024 at 6:04 AM jkl826 ***@***.***> wrote:
g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall
-Wno-sign-compare -pedantic -O3 -std=c++11 -I../include
-I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc
In file included from ../include/genbank.hh:12:0,
from genbank.cc:10:
../include/types.hh:16:43: fatal error: boost/archive/text_oarchive.hpp:
No such file or directory
#include <boost/archive/text_oarchive.hpp>
^
compilation terminated.
make[1]: *** [genbank.o] Error 1
make[1]: Leaving directory
`/home/u041175/workspace/jiakeli/rnaseq/software/new/Augustus-3.5.0/src'
make: *** [augustus] Error 2
I need help
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Maybe you have solved this problem? I met the same one. |
Since installing augustus from source without root previleges wasn't easy for me, I thought posting here the commands I used for installation.
If not already done, install conda, bioconda, and, optional but recommended, mamba (these are useful anyway).
Create and activate a dedicated environment for augustus (or activate an existing one of your choice):
requirements.txtand install them:common.mkwith the correct settings:Tested (not thoroughly) on Ubuntu 18 and CentOS 7 with augustus commit
d1fd097. Note that augustus is also on bioconda but the version there may be outdated. Any feedback most welcome.The text was updated successfully, but these errors were encountered: