New upstream version 6.0.7+dfsg

        proteinortho_grab_proteins.pl speedup for -exact and a given proteinortho file

        proteinortho6.pl replaced chomp with s/[\r\n]+$//

        proteinortho_clustering.cpp fix bug that only uses lapack if -pld is set, regardless of the value.

    11. Sept (uid: 3813)

	updated shebang of ffadj such that python2.7 is used directly (ffadj fails if called with higher version of python)

	-p=blastp is now alias of blastp+ and legacy blast is now -p=blastp_legacy (blastn is equivalent)

	Makefile: static now includes -lquadmath

3697

3813

ifeq ($(USEPRECOMPILEDLAPACK),TRUE)

ifeq ($(STATIC),TRUE)

	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";

	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] ) || ( \

	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -lquadmath -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] ) || ( \

		echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \

		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \

			echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \

# Installation

 **Proteinortho comes with precompiled binaries of all executables (Linux/x86) so just run the proteinortho6.pl in the downloaded directory.**

You could also move all executables to your favorite bin directory (e.g. with make install PREFIX=/home/paul/bin).

 **Proteinortho comes with precompiled binaries of all executables (Linux/x86) so you should be able to run perl proteinortho6.pl in the downloaded directory.**

You could also move all executables to your favorite directory (e.g. with make install PREFIX=/home/paul/bin).

If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.

<br>

<br>

#### Easy installation with dpkg (root privileges are required)

The deb package can be downloaded here: [https://packages.debian.org/unstable/proteinortho](https://packages.debian.org/unstable/proteinortho).

Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`.

<br>

#### *(Easy installation with apt-get)*

**! Disclamer: Work in progress !**

*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `sudo apt-get install proteinortho` (currently this installes the outdated version v5.16b)*

<br>

#### 1. Prerequisites

Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.

     - mmseqs2 (conda install mmseqs2, https://github.com/soedinglab/MMseqs2)

   - Perl v5.08 or higher (to test this, type perl -v in the command line)

   - Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) 

   - Perl modules: Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with `cpan install Thread::Queue` )

   - Perl standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with `cpan install ...` )

</details>

<br>

#### 2. Building and installing proteinortho from source (linux and osx)

  Here you <i>can</i> use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.

  Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.

  If you dont have one (or you have no root permissions), then 'make' will automatically compile a lapack (v3.8.0) for you !

  If you dont have Lapack, then 'make' will automatically compiles Lapack v3.8.0 for you !

  Fetch the latest source code archive downloaded from <a href="https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip">here</a> 

<details> <summary>or from here (Click to expand)</summary>

    <details>

      <summary>show all algorithms (Click to expand)</summary>

        - blastn,blastp,tblastx : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.

        - blastn_legacy,blastp_legacy,tblastx_legacy : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.

        - blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)

        family. The suffix 'n' or 'p' indicates nucleotide or protein input files.

<h1 id="installation">Installation</h1>

<p><strong>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so just run the proteinortho6.pl in the downloaded directory.</strong>

You could also move all executables to your favorite bin directory (e.g. with make install PREFIX=/home/paul/bin).

<p><strong>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so you should be able to run perl proteinortho6.pl in the downloaded directory.</strong>

You could also move all executables to your favorite directory (e.g. with make install PREFIX=/home/paul/bin).

If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.</p>

<p><br></p>

<p><br></p>

<h4 id="easyinstallationwithdpkgrootprivilegesarerequired">Easy installation with dpkg (root privileges are required)</h4>

<p>The deb package can be downloaded here: <a href="https://packages.debian.org/unstable/proteinortho">https://packages.debian.org/unstable/proteinortho</a>.

Afterwards the deb package can be installed with <code>sudo dpkg -i proteinortho*deb</code>.</p>

<p><br></p>

<h4 id="easyinstallationwithaptget"><em>(Easy installation with apt-get)</em></h4>

<p><strong>! Disclamer: Work in progress !</strong>

<em>proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with <code>sudo apt-get install proteinortho</code> (currently this installes the outdated version v5.16b)</em></p>

<p><br></p>

<h4 id="1prerequisites">1. Prerequisites</h4>

<p>Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.</p>

<li><p>Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) </p></li>

<li><p>Perl modules: Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with <code>cpan install Thread::Queue</code> )

<li><p>Perl standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with <code>cpan install ...</code> )

</details></p></li>

</ul>

<h4 id="2buildingandinstallingproteinorthofromsourcelinuxandosx">2. Building and installing proteinortho from source (linux and osx)</h4>

<p>Here you <i>can</i> use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.</p>

<p>Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.</p>

<p>If you dont have one (or you have no root permissions), then 'make' will automatically compile a lapack (v3.8.0) for you !</p>

<p>If you dont have Lapack, then 'make' will automatically compiles Lapack v3.8.0 for you !</p>

<p>Fetch the latest source code archive downloaded from <a href="https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip">here</a> 

<details> <summary>or from here (Click to expand)</summary></p>

<p><details>

  <summary>show all algorithms (Click to expand)</summary></p>

<pre><code>- blastn,blastp,tblastx : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.

<pre><code>- blastn_legacy,blastp_legacy,tblastx_legacy : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.

- blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)

family. The suffix 'n' or 'p' indicates nucleotide or protein input files.