Skip to content

Commit

Permalink
Version 0.99 release candidate released
Browse files Browse the repository at this point in the history
  • Loading branch information
@V-Z
V-Z committed Dec 8, 2015
1 parent 57f9efa commit 6f2b67d
Show file tree
Hide file tree
Showing 10 changed files with 104 additions and 90 deletions.
2 changes: 1 addition & 1 deletion .info
View file
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
CURRENTVERSION=0.99
NEWVERSION=https://github.com/V-Z/sondovac/releases/download/v0.95-beta/sondovac-0.99-rc.zip
NEWVERSION=https://github.com/V-Z/sondovac/releases/download/v0.99-rc/sondovac-0.99-rc.zip
4 changes: 2 additions & 2 deletions CHANGELOG
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,12 @@ Sondovač is a script to create orthologous low-copy nuclear probes from
transcriptome and genome skim data for target enrichment.


Version 0.99 release candidate released 2015-12-07
Version 0.99 release candidate released 2015-12-08
================================================================================

* Fixed error with some input files for part B.
* Finished colorization of command-line user interface.
* Added possibility minimal exon length of the loci.
* Added possibility to set minimal exon length of the loci.
* Various fixes and UI enhancements.
* Improved documentation.

Expand Down
112 changes: 60 additions & 52 deletions INSTALL
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,21 +28,21 @@ Sondovač will check if those programs are installed - available in the PATH
you have those packages installed (in current versions), ensure their binaries
are in PATH. This should not be a problem for basic tools available in any
UNIX-based operating system, as basic installation usually contains all needed
tools. If you lack some of the required tools, the script will notify
you, and you will have to install them manually. If this will be needed, check
the documentation for your operating system.
tools. If you lack some of the required tools, the script will notify you, and
you will have to install them manually. If this will be needed, check the
documentation for your operating system.

If required scientific programs are not installed, Sondovač will offer you
installation. You can use precompiled binaries available together with the
script (this is the recommended option) or (sometimes) from the web. This is
the recommended way. In case you would like to compile required software
script (this is the recommended option) or (sometimes) from the web. This
is the recommended way. In case you would like to compile required software
yourself, the script will guide you through this process. Anyway, this is
recommended only for advanced users, as compilation might sometimes be very
tricky. Users of Mac OS X can install those applications also using Homebrew
(see http://brew.sh/). For compilation you need Apache Ant, GNU G++, GNU GCC,
GIT, Java/OpenJDK, libpng developmental files, and zlib developmental files.
Ensure that you have those tools available - they should be readily available for
any UNIX-based operating system.
Ensure that you have those tools available - they should be readily available
for any UNIX-based operating system.

sondovac_part_a.sh requires (and will install) the following software packages:
* BLAT
Expand All @@ -56,25 +56,27 @@ sondovac_part_b.sh requires (and will install) the following software packages:
* CD-HIT
* BLAT

Geneious is required for step 7 of the pipeline. See below, README and PDF manual for details.
Geneious is required for step 7 of the pipeline. See below, README and PDF
manual for details.

The following UNIX tools are required to run Sondovač. They are usually readily
available in UNIX systems (but see note for Mac OS X below), so there is
usually no need to install them manually. The tools are awk, bc, bunzip2, cat,
cp, curl or wget, cut, dirname, echo, egrep, cd, g++, gcc, grep, gunzip, join, less,
lsb_release or python (for Linux), make, mkdir, perl, pkg-config, pwd, sed, sort, tar, tr, uname,
uniq, unzip, wc.
cp, curl or wget, cut, dirname, echo, egrep, cd, g++, gcc, grep, gunzip, join,
less, lsb_release or python (for Linux), make, mkdir, perl, pkg-config, pwd,
sed, sort, tar, tr, uname, uniq, unzip, wc.

For Mac OS X users, Homebrew (http://brew.sh/) will be installed by the script, and it will
install (new software or newer versions) Apache Ant, BASH (the shell interpreter), GNU AWK, GNU
coreutils, GNU GCC, git, GNU grep, GNU make, pkg-config, GNU sed, and wget. Mac
OS X is missing some tools and for others (typically sed, grep or awk) contains
too old BSD versions. The script will guide the user through the process, and if the
user would wish, it is possible safely and easily remove these tools afterwards.
For Mac OS X users, Homebrew (http://brew.sh/) will be installed by the script,
and it will install (new software or newer versions) Apache Ant, BASH (the
shell interpreter), GNU AWK, GNU coreutils, GNU GCC, git, GNU grep, GNU make,
pkg-config, GNU sed, and wget. Mac OS X is missing some tools and for others
(typically sed, grep or awk) contains too old BSD versions. The script will
guide the user through the process, and if the user would wish, it is possible
safely and easily remove these tools afterwards.

See the PDF manual for details about tools required by Sondovač and their manual
installation. For most users it should be sufficient to be guided by the script
to install needed tools automatically.
See the PDF manual for details about tools required by Sondovač and their
manual installation. For most users it should be sufficient to be guided
by the script to install needed tools automatically.


First launch of Sondovač
Expand All @@ -98,7 +100,8 @@ to see basic usage instructions. See README and PDF manual for more information.
Examples (see README and PDF manual for explanation of command line parameters)
--------------------------------------------------------------------------------

The basic and most simple usage (running in interactive mode, see README and PDF manual):
The basic and most simple usage (running in interactive mode, see README and
PDF manual):

./sondovac_part_a.sh -i

Expand All @@ -119,9 +122,9 @@ Modify parameter "-a", otherwise run interactively:

./sondovac_part_a.sh -i -a 300

Running in non-interactive mode (parameter "-n", see README) - in such case the user
must specify all required input files (parameters "-f", "-c", "-m", "-t" and
"-q"). Moreover, parameter "-y" is modified:
Running in non-interactive mode (parameter "-n", see README) - in such case the
user must specify all required input files (parameters "-f", "-c", "-m", "-t"
and "-q"). Moreover, parameter "-y" is modified:

./sondovac_part_a.sh -n -f input.fa -c referencecp.fasta -m referencemt.fsa \
-t reads1.fastq -q reads2.fastq -y 90
Expand All @@ -131,9 +134,9 @@ need to be specified explicitly:

./sondovac_part_a.sh -s 950

We recommend to launch Sondovač at least for the first time in an interactive mode,
so that the script will verify all requirements and install missing tools when
needed. We then recommend to use non-interactive mode for routine usage.
We recommend to launch Sondovač at least for the first time in an interactive
mode, so that the script will verify all requirements and install missing tools
when needed. We then recommend to use non-interactive mode for routine usage.


Help for usage of terminal
Expand All @@ -156,22 +159,25 @@ first. You can try some of those:
Geneious
================================================================================

Sondovač workflow is divided into three parts (see README and PDF manual for details):
Sondovač workflow is divided into three parts (see README and PDF manual for
details):
1) Raw input data are analyzed by sondovac_part_a.sh.
2) Sequences obtained in part A are assembled by Geneious in a separate step by the user.
2) Sequences obtained in part A are assembled by Geneious in a separate step by
the user.
3) Final probes are produced by sondovac_part_b.sh.

For part (2) of the script the user must have Geneious. We plan to replace it by some free
open-source command line tool in some future release of Sondovač. Visit
http://www.geneious.com/ for download, purchase, installation and usage of
Geneious.
For part (2) of the script the user must have Geneious. We plan to replace it
by some free open-source command line tool in some future release of Sondovač.
Visit http://www.geneious.com/ for download, purchase, installation and usage
of Geneious.


Software links (including required versions)
================================================================================

"X" denotes any subversion of a particular lineage, and "v. >" denotes any version
higher then noted. Generally, any current version should usually be fine.
"X" denotes any subversion of a particular lineage, and "v. >" denotes any
version higher then noted. Generally, any current version should usually be
fine.

* Apache Ant 1.9.X - https://ant.apache.org/
* bam2fastq 1.1.0 - http://gsl.hudsonalpha.org/information/software/bam2fastq
Expand All @@ -198,11 +204,12 @@ Vocabulary

* Binary - An application in a form understandable by the computer, but usually
not transferable among operating systems and/or hardware platforms. Binaries
in Windows usually have the extension *.exe, in UNIX there is usually no extension.
in Windows usually have the extension *.exe, in UNIX there is usually no
extension.
* BASH - "The command line" - fully featured programming scripting language
accessible through the terminal of any UNIX-based operating system (any Linux,
Mac OS X, Solaris, any variant of BSD and more). BASH scripts usually have the
extension *.sh.
accessible through the terminal of any UNIX-based operating system (any
Linux, Mac OS X, Solaris, any variant of BSD and more). BASH scripts usually
have the extension *.sh.
* BSD - Group of popular UNIX-based operating systems. See
https://en.wikipedia.org/wiki/Berkeley_Software_Distribution.
* C - Popular programming language. Source code must be compiled for each
Expand All @@ -222,10 +229,10 @@ Vocabulary
its free community testing platform. See https://getfedora.org/.
* GNU - Major project providing free software widely used in many operating
systems, see https://gnu.org/.
* Homebrew - Tool primarily for Mac OS X (although there is also a Linux version
available) replacing the practically missing package manager for this system. Can
be used to install plenty of various applications as well as updating tools
already available in Mac OS X. See http://brew.sh/.
* Homebrew - Tool primarily for Mac OS X (although there is also a Linux
version available) replacing the practically missing package manager for this
system. Can be used to install plenty of various applications as well as
updating tools already available in Mac OS X. See http://brew.sh/.
* Java - Very popular programming language. It requires Java runtime
environment to be installed, but the applications are very well transferable
among operating systems. See https://www.java.com/.
Expand All @@ -243,9 +250,9 @@ Vocabulary
http://linuxmint.com/.
* Mac OS X - Popular operating system produced by Apple. The system kernel is
based on UNIX, see https://www.apple.com/osx/.
* Open-source - Generally, the source code of an application is available together
with the application and can, under certain conditions, be defined in license
modified, redistributed etc. See
* Open-source - Generally, the source code of an application is available
together with the application and can, under certain conditions, be defined
in license modified, redistributed etc. See
https://en.wikipedia.org/wiki/Free_and_open-source_software.
* openSUSE - Popular Linux distribution, see https://www.opensuse.org/.
* Operating system - Basic system running on your computer - typically MS
Expand All @@ -262,7 +269,8 @@ Vocabulary
used only in particular cases. In case of shell applications, parameters are
usually given such as "application -X", "application -parameter",
"application -Param SomeValue" and so on. See manual for particular
application (e.g. "man application"), in case of Sondovač see README and PDF manual.
application (e.g. "man application"), in case of Sondovač see README and PDF
manual.
* PATH - Directories in the computer where the system looks for installed
software (in a UNIX-based system you can view it by the command "echo
$PATH"). If you need to modify it manually, see the documentation for your
Expand All @@ -288,9 +296,9 @@ Vocabulary
http://distrowatch.com/table.php?distribution=solaris.
* Source code - Human-readable code written in any text editor used to develop
any application. Applications written in interpreted languages (BASH, Perl,
Python, ...) can be distributed just in form of a source code (nothing else is
required). Other programming languages (C, C++, ...) require compilation to
get fully functional application.
Python, ...) can be distributed just in form of a source code (nothing else
is required). Other programming languages (C, C++, ...) require compilation
to get fully functional application.
* SUSE Linux Enterprise (SLE) - Large Linux company providing mainly solutions
for big companies. See https://www.suse.com/.
* Terminal - See "Shell".
Expand All @@ -305,5 +313,5 @@ Vocabulary
problems, no one will probably help you. Moreover, using old versions of
software can be a security risk because of security issues fixed in newer
versions.
* Variable - Named value storing various information, one of the basic part of any
programming language, application, operating system.
* Variable - Named value storing various information, one of the basic part of
any programming language, application, operating system.
12 changes: 6 additions & 6 deletions LICENSE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@ Sondovač 0.99 RC Licenses
Sondovač is a script to create orthologous low-copy nuclear probes from
transcriptome and genome skim data for target enrichment.

The set of BASH scripts Sondovač is licensed under GNU General Public License
version 3. List of licenses of included software is in following table (see
full texts below). License of BLAT does not allow redistribution, so that this
software is not included and the software is downloaded on the fly. Script is
also using software included in GNU core utilities (basic tools available in any
UNIX-based system), see https://www.gnu.org/software/coreutils/ for details.
The set of BASH scripts Sondovač is licensed under GNU General Public License
version 3. List of licenses of included software is in following table (see
full texts below). License of BLAT does not allow redistribution, so that this
software is not included and the software is downloaded on the fly. Script is
also using software included in GNU core utilities (basic tools available in
any UNIX-based system), see https://www.gnu.org/software/coreutils/ for details.

Software License License details
--------------------------------------------------------------------------------
Expand Down
17 changes: 9 additions & 8 deletions README
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
Sondovač 0.99 RC Basic help

Sondovač (English pronunciation is "Sondovach") is a script to create
orthologous low-copy nuclear probes from transcriptome and genome skim data for
target enrichment.
Sondovač (English pronunciation is "Sondovach". The word is a Czech neologism
meaning something like "The Prober" or "The Probe Maker".) is a script to
create orthologous low-copy nuclear probes from transcriptome and genome skim
data for target enrichment.


Script summary
Expand Down Expand Up @@ -173,8 +174,8 @@ process its output manually by Geneious according to the instructions given
below. The output of Geneious is then processed by sondovac_part_b.sh, which
produces the final probe set. Geneious was tested with versions 6, 7 and 8.

Import the output file of part A of the script (sondovac_part_a.sh): go to menu
File | Import | From File... This file is named as:
Import the output file of part A of the script (sondovac_part_a.sh):
go to menu File | Import | From File... This file is named as:
*_blat_unique_transcripts_versus_genome_skim_data-no_missing_fin.fsa

Select the file and go to menu Tools | Align / Assemble | De Novo Assemble.
Expand Down Expand Up @@ -274,8 +275,7 @@ Input files:
Optional parameters:
See chapter "Pipeline" for steps referred here.
If those parameters are not provided, the default values are used, and it is
not
possible to change them any time later (not even in interactive mode).
not possible to change them any time later (not even in interactive mode).

-a ### Maximum overlap length expected in approximately ≥90% of read pairs
(parameter -M of FLASH, see its manual for details). FLASH can not
Expand Down Expand Up @@ -432,7 +432,8 @@ Script sondovac_part_b.sh creates the following files:
3) *_target_enrichment_probe_sequences.fasta - Probes in FASTA.
4) *_possible_cp_dna_genes_in_probe_set.pslx - In case of any BLAT hits, the
user might needs to manually remove these plastid probe sequences from
*_target_enrichment_probe_sequences.fasta (the previous script outfile); the remaining ones are the final probe sequences in FASTA.
*_target_enrichment_probe_sequences.fasta (the previous script outfile);
the remaining ones are the final probe sequences in FASTA.

An asterisk (*) denotes the beginning of the output files' names specified by
the user with parameter "-o". If user does not select a custom name, default
Expand Down
Binary file modified manual/sondovac_manual.pdf
View file
Binary file not shown.
Loading

0 comments on commit 6f2b67d

Please sign in to comment.