I am trying to setup PSIPRED to run a secondary structure prediction but the README.md file is not detailed enough for a beginner like me to setup and run PSIPRED. I am trying to use it with BLAST+.
I am on a Linux Ubuntu 17.04 operating system, and the following are the steps I take to try and setup PSIPRED. There seems to be missing programs that I am not sure how to install or find where they are as well as missing commands:
sudo apt install ncbi-blast+ #OK: Install BLAST+
wget http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.01.tar.gz #OK: Get the latest PSIPRED
tar xzvf psipred.4.01.tar.gz #OK: Extract the latest PSIPRED
rm psipred.4.01.tar.gz #OK: Remove the the latest PSIPRED .tar.gz download
cd psipred/src #OK: Go to source code directory
make #OK: Compile PSIPRED binaries
make install #OK: Compile PSIPRED binaries
cd .. #OK: Go back to PSIPRED top level directory
wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz #OK: Download the latest uniref90 database
gunzip -v uniref90.fasta.gz #OK: Uncompress the latest uniref90 database
bin/pfilt uniref90.fasta > uniref90filt #ERROR HERE: pfilt not found. Cannot find where the pfilt program is and cannot find from where to install it from
formatdb -t uniref90filt -i uniref90filt #ERROR HERE: formatdb not found. Cannot find where the formatdb program is and cannot find from where to install it from
makeblastdb -dbtype prot -in uniref90filt -out uniref90filt #OK: Not sure what this does but it works fine
./BLAST+/runpsipredplus example/example.fasta #ERROR HERE: /usr/local/bin/psiblast: Command not found. FATAL: Error whilst running blastpgp - script terminated!
How can I get PSIPRED to work? what I am doing wrong? Where can I get all the necessary external program to make PSIPRED work? What am I missing?
Related
I am trying to solve problem installing XMind 3.6.0 RPM on Fedora 23.
I have downloaded the .deb package from XMind webpage.
Than, I have converted it to RPM package with Alien, to be able to install it on Fedora with help of this manual.
sudo alien -r -c xmind-3.6.0-2.x86_64.deb
and than install the generated RPM package
sudo rpm -ivh xmind-3.6.0-2.x86_64.rpm
but I keep getting the error message:
Preparing... ################################# [100%]
file /usr/bin from install of xmind-3.6.0-2.x86_64 conflicts with file from package filesystem-3.2-35.fc23.x86_64
file /usr/lib from install of xmind-3.6.0-2.x86_64 conflicts with file from package filesystem-3.2-35.fc23.x86_64
Does anybody know, how to resolve this conflict?
Thanks,
shimon
I was unable to solve the error described in my post. However, I have found a way to install XMind 7 (3.6.0) on Fedora 23.
Following this page.
The problem is, the xmind binaries structure has changed since this article. So the commands needed are little bit different.
Download Xmind portable version from Xmind web page - http://www.xmind.net/xmind/downloads/xmind7-portable-3.6.0.R-201511090408.zip
Extract it to directory ~/xmind_portable, then cd ~/xmind_portable
Untar the data.tar.gz tar -xf data.tar.gz
Move desktop launcher sudo mv ./usr/share/applications/xmind.desktop /usr/share/applications
sudo mv ./usr/share/mime/packages/xmind.xml /usr/share/mime/packages/
Move application data sudo mv ./usr/lib/xmind/ /opt/
Update mime DB sudo update-mime-database /usr/share/mime/
Make a link to your bin
sudo ln -s /opt/xmind/XMind /usr/local/bin/xmind
Then use it!
xmind
I'm trying to build from source MariaDB on CentOS 7. I have only done the following commands before I get the error shown in this image:
$ cd /usr/local/src
$ wget https://downloads.mariadb.org/interstitial/mariadb-5.5.40/source/mariadb-5.5.40.tar.gz/from/http%3A//ftp.ddg.lth.se/mariadb
$ tar xzvf mariadb
$ cd mariadb-5.5.40/
$ chown -R root.root .
$ cmake . -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/mariadb
proof that libaio-devel is installed
For anyone that is in a similar situation, cmake apparently does a pretty bad job of re-checking dependencies, even removing the cache file doesn't work very well.
Just delete and re-extract from the .tar.gz and then cmake again, if you actually have the dependencies then they will be found.
I'd like to install the following UDF's from sam J levy's site
I have run through the windows (32 bit) installation with wamp for my testing server with no problem. Now I have my proper server running centOs 6.4. I have copied the .so files to
usr/lib64/mysql/plugin/damlev.so
I then try to run one of the sql statements to create the function
CREATE FUNCTION damlev RETURNS INTEGER SONAME 'damlev.so';
And get the following error
1126 - Can't open shared library 'damlev.so' (errno: 22 /usr/lib64/mysql/plugin/damlev.so: wrong ELF class: ELFCLASS32)
What Am I doing wrong. Is it because the server is 64bit?
Edit Bounty Started:
If more details about the server are required I can gladly supply them. I need this function installed.
It seems that you're trying to use the damlev.so library included in the damlev.zip file of the Levi's site, but that library is for an Ubuntu 32-bit system, therefore it cannot work on your Centos 64-bit system, so you'll have to compile from sources.
As a prerequisite, you must install the g++ compiler and the mysql development libraries:
yum install gcc-c++ mysql-devel
Also, if you don't have wget and unzip, install them with the following command:
yum install wget unzip
Then download the source code and unzip it somewhere:
cd tmp
mkdir damlev
cd damlev
wget http://samjlevy.com/wp-content/uploads/2011/03/damlev.zip
unzip damlev.zip
cd src
Finally compile, install the plugin and restart the mysql server:
g++ -fPIC -I /usr/include/mysql/ -o damlev.so -shared damlev.cpp
cp damlev.so /usr/lib64/mysql/plugin/
service mysql restart
Please note that all the above command must be run as "root".
I want to build a modified version of lighttpd.
I follow this tutorial:
http://h264.code-shop.com/trac/wiki/Mod-H264-Streaming-Lighttpd-Version2
This is what I've done so far
apt get install lighttpd
apt get install automake autoconf libtool
cd /var/tmp
wget http://h264.code-shop.com/download/lighttpd-1.4.18_mod_h264_streaming-2.2.9.tar.gz
tar -zxvf lighttpd-1.4.18_mod_h264_streaming-2.2.9.tar.gz
wget http://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-1.4.28.tar.gz
tar ...
after I copied all files and data to the directory and Makefile.am I entered:
./autogen.sh
./configure --enable-maintainer-mode --prefix=${HOME}/test/lighttpd-1.4.28
the console returnes:
...
checking for pkg-config... no
checking for libev support... ./configure: line 12184: syntax error near unexpected token `LIBEV,'
./configure: line 12184: ` PKG_CHECK_MODULES(LIBEV, libev, ,'
root#foo...
Some people solved this by installing "pkg-config". I installed this package but I still can't run the configuration.
I just found out that this version of lighttpd contains a bug. I switched from 1.4.28 to 1.4.30 and everything went good.
I'm trying to compile a C++ program and one of the classes uses . g++ is not able to find the libraries would be my guess. The command i use to compile is -
g++ c1.cpp c2.cpp c3.cpp c4.cpp -o c4 -lm -lmysqlclient
c3.cpp is the file that needs mysql.h. This works perfectly on my local machine, but refuses to run on the server with the error
cannot find -lmysqlclient
I tried finding the libmysqlclient.so files on the server using the find command, I don't think they are present there
uname -a
reveals
SunOS opteron 5.10 Generic_139556-08 i86pc i386 i86pc
user#opteron 12:26:02 ~/c++/projname/
I realize that i need to link some libraries, but where and how?
Any help would be appreciated.
Thanks.
Whatever library packages u think is not installed can be installed using sudo apt-get install. But the problem is to find the right name of the package apt-get can understand. So how to do that ?! simple
use command : sudo apt-cache search <filename>
For eg.: in this case lmysqlclient
sudo apt-cache search mysqlclient
(remember to exclude 'l' from the actual name ,ie, mysqlclient and not lmysqlclient).
This outputs:
libmysqlclient-dev - MySQL database development files
In the above -libmysqlclient-dev is the name that apt-get can recognize and solve our cannot find lmysqlclient problem
so now type: sudo apt-get install libmysqlclient-dev from interface.
After its done, try making your required file.
Simplifying #SriHariY.S's answer-
Try installing it with sudo apt-get install libmysqlclient-dev.
Do you have the MySQL client libraries? Can you look for it as
find / -name "libmysqlclient.so" -type f -print 2>/dev/null
Also, you can use the -R flag on linker to hardlink the libmysqlclient as
g++ -R/usr/local/mysql/lib ....
Or, you can export the LD_LIBRARY_PATH_32 or LD_LIBRARY_PATH_64 as
export LD_LIBRARY_PATH_32=$MYSQL_HOME/lib
Urko,
On Ubuntu 18 I used this command to find a name of required package for fixing this error:
apt search lmysqlclient
After this I installed missing package:
sudo apt install libmariadbclient-dev-compat