The file install.sh is an executable file for installing Ribovore
and its dependencies. That file is located online at github.
To install the latest version of Ribovore download this file:
https://raw.githubusercontent.com/ncbi/ribovore/master/install.sh
To download any specific release/version, for example version 1.0 download
the corresponding install.sh file for that release/version.
https://raw.githubusercontent.com/ncbi/ribovore/1.0/install.sh
Copy the install.sh file into the directory in which you want
to install Ribovore. A good name for that directory is
ribovore-install. Then move into that directory and run the install
script. There are six possible ways to run install.sh and its usage can be
viewed by executing the script without any arguments:
>sh ./install.sh
Usage: ./install.sh <os>
or
Usage: ./install.sh <os> keep
valid options for <os> are:
"linux": full install for linux
"macosx-intel": full install for macosx-intel
"macosx-silicon": full install for macosx-silicon
"rt-linux": ribotyper only for linux
"rt-macosx-intel": ribotyper only for macosx-intel
"rt-macosx-silicon": ribotyper only for macosx-silicon
use "keep" as 2nd argument to keep nonessential files
which are normally removed
The command you should use for installation depends on your
operating system and whether or not you want to install the full
Ribovore package or just want to use the ribotyper script.
For example, to install on a linux machine, execute:
sh ./install.sh linux
The linux, macosx-intel, or macosx-silicon argument controls the
type of infernal and blast executable files that will be installed and
also dictates whether the vecscreen_plus_taxonomy package will be
installed. vecscreen_plus_taxonomy will be installed only for
linux installations and consequently only linux installations will
be able to use all features of ribodbmaker. Mac/OSX installations
will be able to run ribodbmaker but only with specific flags that
cause steps that require executable programs that get installed with
vecscreen_plus_taxonomy to be skipped, as explained more here.
The install.sh command will create several directories in the
current directory. It will download and install Ribovore and the
required module libraries
sequip, as well as the binary
executables of Infernal, the NCBI
BLAST package (for either Linux or Mac/OSX), and (if Linux) the
vecscreen_plus_taxonomy
package.
The installation procedure will remove some unnecessary files from the
dependencies it installs (infernal and blast) by default, but these
files can be kept if you additionally add keep as an additional
argument, for example:
sh ./install.sh linux keep
When install.sh is finished running it will print important
instructions to the screen that explain how to modify your environment
variables so that you can run the Ribovore scripts, as discussed next.
As mentioned above, when you run install.sh, instructions will be
output about how to change your environment variables so that you can
run the Ribovore scripts. Those instructions are also included below for
reference, but without the actual path to where you ran install.sh
(below it is replaced with <full path to directory in which you ran install.sh>)
The final step is to update your environment variables.
(See ribovore/README.txt for more information.)
If you are using the bash or zsh shell add the following lines to
the end of your '.bashrc' or '.zshrc' file in your home directory:
export RIBOINSTALLDIR="<full path to directory in which you ran install.sh>"
export RIBOSCRIPTSDIR="$RIBOINSTALLDIR/ribovore"
export RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries"
export RIBOEASELDIR="$RIBOINSTALLDIR/infernal/binaries"
export RIBOSEQUIPDIR="$RIBOINSTALLDIR/sequip"
export RIBOTIMEDIR="/usr/bin"
export RIBOBLASTDIR="$RIBOINSTALLDIR/ncbi-blast/bin"
export RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor"
export VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy"
export BLASTDB="$VECPLUSDIR/univec-files":"$RRNASENSORDIR":"$BLASTDB"
export PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB"
export PATH="$RIBOSCRIPTSDIR":"$RIBOBLASTDIR":"$RRNASENSORDIR":"$PATH"
After adding the export lines to your .bashrc or .zshrc file, source that file
to update your current environment with the command:
source ~/.bashrc
OR
source ~/.zshrc
---
If you are using the C shell, add the following
lines to the end of your '.cshrc' file in your home
directory:
setenv RIBOINSTALLDIR "<full path to directory in which you ran install.sh>"
setenv RIBOSCRIPTSDIR "$RIBOINSTALLDIR/ribovore"
setenv RIBOINFERNALDIR "$RIBOINSTALLDIR/infernal/binaries"
setenv RIBOEASELDIR "$RIBOINSTALLDIR/infernal/binaries"
setenv RIBOSEQUIPDIR "$RIBOINSTALLDIR/sequip"
setenv RIBOTIMEDIR "/usr/bin"
setenv RIBOBLASTDIR "$RIBOINSTALLDIR/ncbi-blast/bin"
setenv RRNASENSORDIR "$RIBOINSTALLDIR/rRNA_sensor"
setenv VECPLUSDIR "$RIBOINSTALLDIR/vecscreen_plus_taxonomy"
setenv BLASTDB "$VECPLUSDIR/univec-files":"$RRNASENSORDIR":"$BLASTDB"
setenv PERL5LIB "$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB"
setenv PATH "$RIBOSCRIPTSDIR":"$RIBOBLASTDIR":"$RRNASENSORDIR":"$PATH"
After adding the setenv lines to your .cshrc file, source that file
to update your current environment with the command:
source ~/.cshrc
(To determine which shell you use, type: 'echo $SHELL')
For Mac/OSX installations, the VECPLUSDIR line will be omitted,
the BLASTDB lines will not include $VECPLUSDIR/univec-files,
and the PERL5LIB line will not include $VECPLUSDIR.
If you use bash or zsh, change the PERL5LIB and/or BLASTDB line in your ~/.bashrc or
~/.zshrc file to:
export PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR"
export BLASTDB="$VECPLUSDIR/univec-files":"$RRNASENSORDIR"
or if you use C shell, change the PERL5LIB line in your ~/.cshrc
file to:
setenv PERL5LIB "$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR"
setenv BLASTDB "$VECPLUSDIR/univec-files":"$RRNASENSORDIR"
And then execute source ~/.bashrc, source ~/.zshrc, or source ~/.cshrc again.
Ribovore includes some tests you can run after setting your environment variables as explained above to make sure that your installation was successful and that your environment variables are set correctly.
These are several shell scripts for running tests; with respect to the
installation directory they are in the directory ribovore/testfiles/ and
start with do- and end with .sh.
You should run the $RIBOSCRIPTSDIR/testfiles/do-all-tests.sh script
to make sure Ribovore installed correctly. They should pass, as shown
below.
There is also a special test script do-parallel-tests.sh that you
should run if you want to test if you can use the -p option with
ribotyper, ribosensor, riboaligner or ribodbmaker for
parallelization on a cluster. But this test will likely only work
internally at NCBI. See this example
for more information. do-parallel-tests.sh is not run as part
of do-all-tests.sh.
To run all tests, execute:
$RIBOSCRIPTSDIR/testfiles/do-all-tests.sh
This script can take up to several minutes to run. If something goes wrong, the script will likely exit quickly.
Below is an example of the expected output for
do-all-tests.sh for a linux installation:
# ribotest :: test ribovore scripts [TEST SCRIPT]
# ribovore 1.0 (Feb 2021)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# date: Wed Feb 3 18:02:23 2021
# $RIBOSCRIPTSDIR: /usr/local/src/ribovore-install/ribovore
#
# test file: /usr/local/src/ribovore-install/ribovore/testfiles/ribotyper.testin
# output directory name: rt-test
# forcing directory overwrite: yes [-f]
# if output files listed in testin file already exist, remove them: yes [--rmout]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Running command 1 [ ribotyper-1-16] ... done. [ 8.2 seconds]
# checking test-16/test-16.ribotyper.short.out ... pass
# checking test-16/test-16.ribotyper.long.out ... pass
# removing directory test-16 ... done
# Running command 2 [ ribotyper-2-100] ... done. [ 22.6 seconds]
# checking r100/r100.ribotyper.short.out ... pass
# checking r100/r100.ribotyper.long.out ... pass
# removing directory r100 ... done
#
#
# PASS: all 4 files were created correctly.
#
#
# List and description of all output files saved in: rt-test.ribotest.list
# Output printed to screen saved in: rt-test.ribotest.log
# List of executed commands saved in: rt-test.ribotest.cmd
#
# All output files created in directory ./rt-test/
#
# Elapsed time: 00:00:30.99
# hh:mm:ss
#
[ok]
Success: all tests passed [do-ribotyper-tests.sh]
# ribotest :: test ribovore scripts [TEST SCRIPT]
# ribovore 1.0 (Feb 2021)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# date: Wed Feb 3 18:02:54 2021
# $RIBOSCRIPTSDIR: /usr/local/src/ribovore-install/ribovore
#
# test file: /usr/local/src/ribovore-install/ribovore/testfiles/riboaligner.testin
# output directory name: ra-test
# forcing directory overwrite: yes [-f]
# if output files listed in testin file already exist, remove them: yes [--rmout]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Running command 1 [ riboaligner-1-16] ... done. [ 13.9 seconds]
# checking test-16-2/test-16-2.riboaligner.tbl ... pass
# checking test-16-2/test-16-2.riboaligner.SSU.Bacteria.partial.stk ... pass
# checking test-16-2/test-16-2.riboaligner.SSU.Bacteria.partial.list ... pass
# checking test-16-2/test-16-2.riboaligner.SSU.Bacteria.partial.ifile ... pass
# checking test-16-2/test-16-2.riboaligner.SSU.Bacteria.partial.elfile ... pass
# removing directory test-16-2 ... done
# Running command 2 [ riboaligner-2-100] ... done. [ 85.7 seconds]
# checking r100-2/r100-2.riboaligner.tbl ... pass
# checking r100-2/r100-2.riboaligner.SSU.Eukarya.partial.list ... pass
# checking r100-2/r100-2.riboaligner.SSU.Eukarya.partial.ifile ... pass
# checking r100-2/r100-2.riboaligner.SSU.Eukarya.partial.elfile ... pass
# checking r100-2/r100-2.riboaligner.SSU.Eukarya.partial.stk ... pass
# removing directory r100-2 ... done
#
#
# PASS: all 10 files were created correctly.
#
#
# List and description of all output files saved in: ra-test.ribotest.list
# Output printed to screen saved in: ra-test.ribotest.log
# List of executed commands saved in: ra-test.ribotest.cmd
#
# All output files created in directory ./ra-test/
#
# Elapsed time: 00:01:40.43
# hh:mm:ss
#
[ok]
Success: all tests passed [do-riboaligner-tests.sh]
# ribotest :: test ribovore scripts [TEST SCRIPT]
# ribovore 1.0 (Feb 2021)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# date: Wed Feb 3 18:04:36 2021
# $RIBOSCRIPTSDIR: /usr/local/src/ribovore-install/ribovore
#
# test file: /usr/local/src/ribovore-install/ribovore/testfiles/ribosensor.testin
# output directory name: rs-test
# forcing directory overwrite: yes [-f]
# if output files listed in testin file already exist, remove them: yes [--rmout]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Running command 1 [ ribosensor-1-16] ... done. [ 14.5 seconds]
# checking test-rs-16/test-rs-16.ribosensor.out ... pass
# checking test-rs-16/test-rs-16.ribosensor.gbank ... pass
# removing directory test-rs-16 ... done
# Running command 2 [ ribosensor-2-100] ... done. [ 42.5 seconds]
# checking rs-r100/rs-r100.ribosensor.out ... pass
# checking rs-r100/rs-r100.ribosensor.gbank ... pass
# removing directory rs-r100 ... done
#
#
# PASS: all 4 files were created correctly.
#
#
# List and description of all output files saved in: rs-test.ribotest.list
# Output printed to screen saved in: rs-test.ribotest.log
# List of executed commands saved in: rs-test.ribotest.cmd
#
# All output files created in directory ./rs-test/
#
# Elapsed time: 00:00:57.31
# hh:mm:ss
#
[ok]
Success: all tests passed [do-ribosensor-tests.sh]
# ribotest :: test ribovore scripts [TEST SCRIPT]
# ribovore 1.0 (Feb 2021)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# date: Wed Feb 3 18:05:34 2021
# $RIBOSCRIPTSDIR: /usr/local/src/ribovore-install/ribovore
#
# test file: /usr/local/src/ribovore-install/ribovore/testfiles/ribodbmaker-vec.testin
# output directory name: rdb-test
# forcing directory overwrite: yes [-f]
# if output files listed in testin file already exist, remove them: yes [--rmout]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Running command 1 [ribodbmaker-vec-1-100] ... done. [ 145.4 seconds]
# checking db100vec/db100vec.ribodbmaker.rdb.tbl ... pass
# removing directory db100vec ... done
#
#
# PASS: all 1 files were created correctly.
#
#
# List and description of all output files saved in: rdb-test.ribotest.list
# Output printed to screen saved in: rdb-test.ribotest.log
# List of executed commands saved in: rdb-test.ribotest.cmd
#
# All output files created in directory ./rdb-test/
#
# Elapsed time: 00:02:25.70
# hh:mm:ss
#
[ok]
Success: all tests passed [do-ribodbmaker-tests.sh]
# ribotest :: test ribovore scripts [TEST SCRIPT]
# ribovore 1.0 (Feb 2021)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# date: Wed Feb 3 18:08:00 2021
# $RIBOSCRIPTSDIR: /usr/local/src/ribovore-install/ribovore
#
# test file: /usr/local/src/ribovore-install/ribovore/testfiles/github-issues/iss1/iss1.testin
# output directory name: iss1-out
# forcing directory overwrite: yes [-f]
# if output files listed in testin file already exist, remove them: yes [--rmout]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Running command 1 [ iss1-ribodb] ... done. [ 11.9 seconds]
# checking db1/db1.ribodbmaker.rdb.tbl ... pass
# removing directory db1 ... done
#
#
# PASS: all 1 files were created correctly.
#
#
# List and description of all output files saved in: iss1-out.ribotest.list
# Output printed to screen saved in: iss1-out.ribotest.log
# List of executed commands saved in: iss1-out.ribotest.cmd
#
# All output files created in directory ./iss1-out/
#
# Elapsed time: 00:00:12.03
# hh:mm:ss
#
[ok]
Success: all tests passed [do-iss1-tests.sh]
Success: all tests passed [do-all-issue-tests.sh]
Success: all tests passed [do-all-tests.sh]
The most important line is the final line:
Success: all tests passed
This means that the test has passed. You should see similar lines if you run the other tests. If you do not and need help figuring out why, email me at eric.nawrocki@nih.gov.