document configure switches

EvolBioInf · Dec 4, 2019 · e028a5e · e028a5e
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diff --git a/Readme.md b/Readme.md
@@ -7,7 +7,7 @@ This is the `phylonium` program for estimating the evolutionary distances betwee
 
 This program depends on two external libraries: [libdivsufsort](https://github.com/y-256/libdivsufsort) and the [GSL](https://www.gnu.org/software/gsl/). Both should be available for installation through a package manager of your choice. Furthermore, to build from the git repository the autotools are required.
 
-Assuming all prerequisites are installed, the build can be started as follows.
+Assuming all prerequisites are installed, the build can be started as follows. See the manual in case of compilation errors or when you try to compile on Arm: [manual](documentation/manual.pdf).
 
     $ autoreconf -fi -Im4
     $ ./configure

diff --git a/documentation/etefmt.py b/documentation/etefmt.py
@@ -78,7 +78,7 @@ def read_names(names_file):
 		out_format = Path(args.image_file).suffix[1:]
 	else:
 		# split input file name
-		print args.file
+		print(args.file)
 		inputfile = Path(args.file if args.file else "etefmt.pdf")
 		out_stem = Path(inputfile).stem
 		out_format = "pdf"

diff --git a/documentation/manual.pdf b/documentation/manual.pdf
diff --git a/documentation/manual.tex b/documentation/manual.tex
@@ -42,7 +42,7 @@
 Biology textbooks usually contain a two part workflow to reconstruct the phylogenetic history of biological sequences: % \cite{fixme}
 First, align the sequences and then use a maximum likelihood approach to find the best tree. This method worked well for many years but has become less useful as the number of sequenced genomes grew rapidly and made existing workflows computationally unfeasible. To mitigate this problem so-called \emph{alignment-free} methods have been devised that quickly estimate phylogenies from unaligned sequences at reasonable accuracy. This document explains how to use one of these tools, \phylonium, for phylogeny reconstruction. 
 
-\section{Installation}
+\section{Installation from Source}
 
 \phylonium has two runtime prerequisites: \tool{libdivsufsort} and the \tool{GNU Scientific Library} (GSL). Install them via your package manager, for instance \lstinline!apt!.
 
@@ -75,6 +75,10 @@ \section{Installation}
 %  ./configure
 \end{lstlisting}
 
+\begin{quotation}
+\textbf{Note:} \phylonium uses x86 specific instructions to speed up the comparison of sequences. If you have a different CPU (e.\,g. arm), you should use \lstinline!./configure --disable-x86simd!. On old x86 systems with old compilers you may have to disable the optimizations for AVX512: \lstinline!./configure --disable-avx512!.
+\end{quotation}
+
 The configuration step fails if \tool{libdivsufsort} or the \tool{GSL} are not found. After successful configuration the program has to be compiled.
 
 \begin{lstlisting}
@@ -123,7 +127,7 @@ \section{Basic Usage}
 Now your working directory contains 29 individual genomic files with the extension \lstinline!.fa!. We begin by comparing only two of them.
 
 \begin{lstlisting}
-%  phylonium FM180568.fa BA000007.fa 
+%  phylonium FM180568.fa BA000007.fa
 2
 BA000007  0.0000e+00  2.4833e-02
 FM180568  2.4833e-02  0.0000e+00
@@ -140,7 +144,7 @@ \section{Basic Usage}
 \begin{lstlisting}
 %  mat nj eco29.out > eco29.tree
 %  cat eco29.tree
-((((((((AE005174:-0.000019,BA000007:1.8692e-04)100:0.000738,CP001846:7.8208e-04)100:0.005264,CP000034:7.1481e-03)100:0.002179,((((((AE014075:0.003805,CU928162:4.0811e-03)30:0.000106,((CP000243:0.000287,CP000468:2.8884e-04)92:0.000463,CU928161:6.3318e-04)100:3.3526e-03)84:0.000290,CP000247:4.3563e-03)100:0.001366,FM180568:5.7901e-03)100:0.006161,(CU928164:0.006473,CP000970:6.6616e-03)100:2.9194e-03)100:0.001377,CU928163:9.6085e-03)100:3.7311e-03)100:0.001825,((((AP009048:0.000021,U00096:-1.2518e-05)100:0.000054,CP001396:5.3536e-05)42:0.000005,CP000948:-1.0385e-05)100:0.004145,(CP000802:0.002660,CP000946:3.0406e-03)100:8.5194e-04)100:1.8943e-03)60:0.000689,((AE005674:0.000240,AE014073:7.9630e-05)100:0.000401,CP000266:5.1491e-04)100:6.4057e-03)78:0.000581,((AP009240:0.003100,CU928160:2.7860e-03)100:0.000288,CP000800:3.2921e-03)100:1.9029e-03)89:0.000362,CP000038:4.6574e-03,(CP001063:0.001311,CP000036:1.3202e-03)100:3.6383e-03);
+((((((((AE005174:-0.000019,BA000007:1.8692e-04)100:0.000738,CP001846:7.8206e-04)100:0.005264,CP000034:7.1481e-03)100:0.002179,((((((AE014075:0.003806,CU928162:4.0810e-03)30:0.000106,((CP000243:0.000287,CP000468:2.8884e-04)92:0.000463,CU928161:6.3318e-04)100:3.3526e-03)84:0.000290,CP000247:4.3564e-03)100:0.001367,FM180568:5.7900e-03)100:0.006160,(CU928164:0.006474,CP000970:6.6612e-03)100:2.9209e-03)100:0.001376,CU928163:9.6094e-03)100:3.7308e-03)100:0.001825,((((AP009048:0.000021,U00096:-1.2523e-05)100:0.000054,CP001396:5.3529e-05)42:0.000005,CP000948:-1.0393e-05)100:0.004144,(CP000802:0.002662,CP000946:3.0385e-03)100:8.4870e-04)100:1.8957e-03)60:0.000689,((AE005674:0.000240,AE014073:7.9602e-05)100:0.000401,CP000266:5.1495e-04)100:6.4055e-03)78:0.000581,((AP009240:0.003100,CU928160:2.7861e-03)100:0.000288,CP000800:3.2921e-03)100:1.9029e-03)89:0.000362,CP000038:4.6574e-03,(CP001063:0.001312,CP000036:1.3202e-03)100:3.6383e-03);
 \end{lstlisting}
 
 This phylogeny in Newick format, which I am here visualizing using the ETE Toolkit\footnote{\url{http://etetoolkit.org/}}.