[med-svn] [Git][med-team/proteinortho][upstream] New upstream version 6.0.7+dfsg

Andreas Tille gitlab at salsa.debian.org
Mon Sep 16 12:38:11 BST 2019 


Andreas Tille pushed to branch upstream at Debian Med / proteinortho


Commits:
e3d760eb by Andreas Tille at 2019-09-16T10:41:53Z
New upstream version 6.0.7+dfsg
- - - - -


15 changed files:

- CHANGELOG
- CHANGEUID
- Makefile
- README.md
- manual.html
- proteinortho6.pl
- src/proteinortho2html.pl
- src/proteinortho2tree.pl
- src/proteinortho2xml.pl
- src/proteinortho_do_mcl.pl
- src/proteinortho_extract_from_graph.pl
- src/proteinortho_ffadj_mcs.py
- src/proteinortho_formatUsearch.pl
- src/proteinortho_grab_proteins.pl
- src/proteinortho_singletons.pl


Changes:

=====================================
CHANGELOG
=====================================
@@ -217,3 +217,7 @@
         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


=====================================
CHANGEUID
=====================================
@@ -1 +1 @@
-3697
+3813


=====================================
Makefile
=====================================
@@ -132,7 +132,7 @@ ifeq ($(USELAPACK),TRUE)
 ifeq ($(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)"; \


=====================================
README.md
=====================================
@@ -39,8 +39,8 @@ You can also send a mail to lechner at staff.uni-marburg.de.
 
 # 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>
@@ -73,6 +73,21 @@ If you need brew (see [here](https://brew.sh/index_de))
 
 <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.
@@ -94,7 +109,7 @@ Proteinortho uses standard software which is often installed already or is part
      - 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>
@@ -113,9 +128,9 @@ Proteinortho uses standard software which is often installed already or is part
 
 #### 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>
@@ -281,7 +296,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
     <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.


=====================================
manual.html
=====================================
@@ -58,8 +58,8 @@ You can also send a mail to lechner at staff.uni-marburg.de.</p>
 
 <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>
@@ -95,6 +95,20 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,
 
 <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>
@@ -128,7 +142,7 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,
 
 <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>
 
@@ -154,9 +168,9 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,
 
 <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>
@@ -345,7 +359,7 @@ blast. 3 -> run the clustering.</p></li></ul>
 <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.


=====================================
proteinortho6.pl
=====================================
The diff for this file was not included because it is too large.

=====================================
src/proteinortho2html.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #pk
 
 ##########################################################################################


=====================================
src/proteinortho2tree.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ##########################################################################################
 #	  This file is part of proteinortho.


=====================================
src/proteinortho2xml.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use strict;
 use warnings "all";


=====================================
src/proteinortho_do_mcl.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #pk
 
 ##########################################################################################


=====================================
src/proteinortho_extract_from_graph.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use warnings;
 use strict;


=====================================
src/proteinortho_ffadj_mcs.py
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python2.7
 
 from sys import stdout, stderr, exit, argv, maxint
 from copy import deepcopy


=====================================
src/proteinortho_formatUsearch.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use warnings;
 use strict;


=====================================
src/proteinortho_grab_proteins.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #pk
 
 ##########################################################################################


=====================================
src/proteinortho_singletons.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 use strict;
 use warnings "all";
 



View it on GitLab: https://salsa.debian.org/med-team/proteinortho/commit/e3d760eb2d63b78ef61fde488783c2e5aa7a856b

-- 
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/commit/e3d760eb2d63b78ef61fde488783c2e5aa7a856b
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