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-- 19 JAN 17 --
Getting lots of compilation errors with R packages:
e.g '/usr/bin/ld: cannot find -lgfortran'
Assumed this related to not having the required compliation tools. Following:
https://www.cyberciti.biz/faq/centos-rhel-7-redhat-linux-install-gcc-compiler-development-tools/
installed 'Development Tools'
> yum group install "Development Tools"
Downloading packages:
(1/30): diffstat-1.57-4.el7.x86_64.rpm | 34 kB 00:00:00
(2/30): byacc-1.9.20130304-3.el7.x86_64.rpm | 64 kB 00:00:00
(3/30): ctags-5.8-13.el7.x86_64.rpm | 154 kB 00:00:00
(4/30): dwz-0.11-3.el7.x86_64.rpm | 98 kB 00:00:00
(5/30): elfutils-0.163-3.el7.x86_64.rpm | 267 kB 00:00:00
(6/30): bison-2.7-4.el7.x86_64.rpm | 577 kB 00:00:01
(7/30): flex-2.5.37-3.el7.x86_64.rpm | 292 kB 00:00:00
(8/30): gdb-7.6.1-80.el7.x86_64.rpm | 2.4 MB 00:00:00
(9/30): gettext-devel-0.18.2.1-4.el7.x86_64.rpm | 314 kB 00:00:00
(10/30): indent-2.2.11-13.el7.x86_64.rpm | 149 kB 00:00:00
(11/30): cscope-15.8-7.el7.x86_64.rpm | 202 kB 00:00:02
(12/30): intltool-0.50.2-6.el7.noarch.rpm | 58 kB 00:00:00
(13/30): doxygen-1.8.5-3.el7.x86_64.rpm | 3.6 MB 00:00:02
(14/30): gettext-common-devel-0.18.2.1-4.el7.noarch.rpm | 367 kB 00:00:01
(15/30): libquadmath-4.8.5-4.el7.x86_64.rpm | 182 kB 00:00:00
(16/30): libquadmath-devel-4.8.5-4.el7.x86_64.rpm | 45 kB 00:00:00
(17/30): patchutils-0.3.3-4.el7.x86_64.rpm | 103 kB 00:00:00
(18/30): gcc-gfortran-4.8.5-4.el7.x86_64.rpm | 6.6 MB 00:00:01
(19/30): perl-XML-Parser-2.41-10.el7.x86_64.rpm | 222 kB 00:00:00
(20/30): perl-srpm-macros-1-8.el7.noarch.rpm | 3.7 kB 00:00:00
(21/30): rcs-5.9.0-5.el7.x86_64.rpm | 229 kB 00:00:00
(22/30): redhat-rpm-config-9.1.0-68.sl7.noarch.rpm | 77 kB 00:00:00
(23/30): rpm-build-4.11.3-17.el7.x86_64.rpm | 143 kB 00:00:00
(24/30): rpm-sign-4.11.3-17.el7.x86_64.rpm | 43 kB 00:00:00
(25/30): libtool-2.4.2-21.el7_2.x86_64.rpm | 587 kB 00:00:00
(26/30): systemtap-2.8-10.el7.x86_64.rpm | 24 kB 00:00:00
(27/30): swig-2.0.10-4.el7.x86_64.rpm | 1.3 MB 00:00:00
(28/30): systemtap-client-2.8-10.el7.x86_64.rpm | 2.9 MB 00:00:00
(29/30): libgfortran-4.8.5-4.el7.x86_64.rpm | 292 kB 00:00:01
(30/30): systemtap-devel-2.8-10.el7.x86_64.rpm | 1.6 MB 00:00:00
This solved this error but lead to the following:
It appears ncdf is missing.
From elsewhere:
Error, nc-config not found or not executable. This is a script that comes with the
netcdf library, version 4.1-beta2 or later, and must be present for configuration
to succeed.
netCDF is dependent upon: hdf5, zlib and curl:
http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_default:
'The usual way of building netCDF requires the HDF5, zlib, and curl libraries. Versions required are at least HDF5 1.8.9, zlib 1.2.5, and curl 7.18.0 or later.'
-- hdf5 --
From scientificlinux forum post:
http://scientificlinuxforum.org/index.php?showtopic=3225
hdf5 is in epel repo.
So what You must do is:
1 - add epel repo
CODE
# wget http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
# rpm -ivh epel-release-7-5.noarch.rpm
2 - install hdf5
CODE
# yum install hdf5
.
Note download was:
http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-9.noarch.rpm
Actually, it looks like I can just use:
> sudo yum install netcdf-devel
-- 18 JAN 17 --
Need to install libssl for R package devtools
yum install openssl-devel
-- 25 JAN 17 --
Need to install lsb_release
See ./cgat for lsb_release installation
-- 26 JAN 17 --
Need to install readline, postgresql, boost
See ./cgat for installation
-- 28 JAN 17 --
Set up scratch folder (/scratch) and automated clean up for files > 30 days old using instructions here:
https://www.maketecheasier.com/delete-old-files-in-a-folder-automatically-in-linux/
write bash script --> ~/git_repos/SetUp/cleanup_scratch.sh
Then use
> crontab -e
And type * 08 * * * ~/git_repos/SetUp/cleanup_scratch.sh in Vim
to run script every day at 8am (hopefully)
Check crontab jobs with:
> crontab -u tss38 -l
> crontab -l
Need to install graphviz for dot (req. for report building)
> yum install graphviz*
Need to install fonts for cgatreport-test (X11)
Error message:
/home/FILESERVER5/proteomics/tss38/anaconda3/lib/python3.5/site-packages/rpy2/robjects/functions.py:106: UserWarning: Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 11 could not be loaded
Resolve with :
> sudo yum install xorg-x11-fonts-75dpi.noarch
> sudo yum install xorg-x11-fonts-100dpi.noarch
Check:
ls /usr/share/X11/fonts/
total 28
drwxr-xr-x. 2 root root 8192 Jan 27 10:53 100dpi
drwxr-xr-x. 2 root root 8192 Jan 27 10:52 75dpi
drwxr-xr-x. 2 root root 4096 Feb 3 2016 util
-- 31 JAN 17 --
Want to install further fonts (microsoft) -
Follow instructions here:
http://www.dedoimedo.com/computers/centos-7-perfect-desktop-more.html
> sudo yum install curl cabextract xorg-x11-font-utils fontconfig
> sudo rpm -i https://sourceforge.net/projects/mscorefonts2/files/rpms/msttcore-fonts-installer-2.6-1.noarch.rpm
-- 10 FEB 17 --
Previously install java with conda but want to run java as a firefox plugin as well,
therefore removed conda installation and installed manually:
https://www.java.com/en/download/help/linux_x64_install.xml
- essentially just download and append to path
Then to add plugin to firefox followed :
http://www.oracle.com/technetwork/java/javase/manual-plugin-install-linux-136395.html
> mkdir .mozilla/plugins
> cd ~/.mozilla/plugins/
> find /home/FILESERVER5/proteomics/tss38/apps/bio/jre1.8.0_121/ -name "*.so"
> ln /home/FILESERVER5/proteomics/tss38/apps/bio/jre1.8.0_121/lib/amd64/libnpjp2.so .
Restart firefox and tried to confirm it was working using link below but couldn't detect java version. Ensured that javascript was also working (as specified), still no luck. Gave up!
https://www.java.com/en/download/installed.jsp
-- 22 FEB 17 --
Install iotop to monitor I/O:
> yum install iotop
-- 27 FEB 17 --
Install system-config-printer to configure printers!
> yum install system-config-printer
-- 30 MAR 17 --
Install python package ete3 to deal with NCBI taxonomy
http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html