Comments (12)
what's wrong?
from sibelia.
- make install should install Sibelia locally, not fail.
- sudo make install should install Sibelia system-wide
from sibelia.
What is "install locally"? Where should it be installed?
By the way, from our INSTALL.md:
"If you want to install "Sibelia" to a location other than /usr/local/bin,
run CMake with -DCMAKE_INSTALL_PREFIX option set:
cmake ../src -DCMAKE_INSTALL_PREFIX="<install destination>"
from sibelia.
e.g. /usr/local/share/
BTW, in previous versions make install worked fine.
To be more clear, as written in INSTALL.md:
To build and install the program, type following:
cd build
cmake ../src
make install
— it is not working.
First solution — just change 'make install' to 'sudo make install' in INSTALL.md. But it's not a good way, since I don't like to sudo anything if it's not 100% necessary.
Second solution — if you encounter in make 'file cannot create directory: /usr/share/sibelia. Maybe need administrative privileges.', install Sibelia locally (to the current directory) automatically.
from sibelia.
"BTW, in previous versions make install worked fine." This is very strange. It seems that on you machine anyone can write in /usr/local/bin. On all Linux systems that I saw writing to /usr/local/bin is permitted for root only. I don't know about Mac, maybe on Mac anyone can write there by default, or you have changed this manually.
P.S. I hate UNIX.
from sibelia.
I meant that previous version also installed itself into /usr/local/bin by default, and on normal systems it required root rights.
from sibelia.
/usr/local/* is accessible by current user (that's why it's local).
/usr/share is not.
from sibelia.
/usr/local is "local" because it's local to the current machine, not user!
"The /usr/local hierarchy is for use by the system administrator when installing software locally. It needs to be safe from being overwritten when the system software is updated. It may be used for programs and data that are shareable amongst a group of hosts, but not found in /usr.
Locally installed software must be placed within /usr/local rather than /usr unless it is being installed to replace or upgrade software in /usr."
http://www.pathname.com/fhs/pub/fhs-2.3.html#USRLOCALLOCALHIERARCHY
from sibelia.
/usr/local belongs to machine, not to user
It is used for installation programs, which are not fully integrated to system (installing manually, not as a package).
Normally, users without root privelegies cannot modify whole root filesystem, so it is strange, that installation in /usr/local doesn`t fails
In addition, default installation prefix for make install should be /usr/local
from sibelia.
I think that there is nothing to discuss here -- I changed INSTALL.md so that it contains sudo make install
from sibelia.
from sibelia.
http://habrastorage.org/storage1/edcaa898/70b48a52/3072387b/da577538.png
from sibelia.
Related Issues (20)
- Add 'V' to the list of permitted characters
- Compilation failure on Ubuntu Server 15 HOT 7
- Not an issue, just a question. Only bacterial? HOT 1
- recent releases
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- Broken page: http://bioinf.spbau.ru/sibelia/examples HOT 1
- Issue when building from source: lagan HOT 7
- Sibelia not detecting perfect palindrome? HOT 3
- Unable to build from source with GCC 5 HOT 1
- Improve runtime requirements, bundled 3rd-party code and a way to avoid that HOT 2
- sortsequences.py issue HOT 1
- about the manual : Resulting de Bruijn graph and customer set explanation HOT 2
- Repeated markers and repeated contigs information are outputted HOT 2
- Sibelia error: Input is larger than 1 GB, can't proceed HOT 4
- Option to output all sites in the VCF not just variant sites
- Input size is larger than 1gb, can't proceed HOT 2
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