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Author: Andreas Tille <tille@debian.org>
Description: Remove csh from docs
Last-Update: Thu, 23 Jul 2020 20:31:54 +0200
--- a/README
+++ b/README
@@ -68,7 +68,7 @@ format (qry.seq) type the following at t
or
- './run-mummer3.csh ref.seq qry.seq <prefix>'
+ './run-mummer3 ref.seq qry.seq <prefix>'
To produce the following files:
<prefix>.out
--- a/docs/run-mummer1.README
+++ b/docs/run-mummer1.README
@@ -38,10 +38,10 @@ it crashes for that reason, that's not a
required.
To use this system, first compile it by typing 'make' at the
-command line. There is a script, 'run-mummer1.csh', that runs all
+command line. There is a script, 'run-mummer1', that runs all
the steps of aligning two genomes. The script takes these arguments:
- run-mummer1.csh <genome1> <genome2> <tag> [-r]
+ run-mummer1 <genome1> <genome2> <tag> [-r]
The two genomes must DNA sequences in FASTA format. Multi-FASTA
files don't work. The tag is used to create 4 output files,
@@ -60,7 +60,7 @@ not performed.
IMPORTANT: the performance of the program can critically depend on the
minimum MUM length you use. The default is 20bp. If you want to
-change it, do the following: edit the file run-mummer1.csh. Add a new
+change it, do the following: edit the file run-mummer1. Add a new
length switch to the 'mummer' call.
The other file - one that we often spend lots of time analyzing - is
@@ -90,8 +90,8 @@ Files in this directory:
gaps.cc Finds longest consistent set of matches in list
produced by mummer1 program.
- run-mummer1.csh Script to run alignment programs. Format is:
- run-mummer1.csh <genome1> <genome2> <tag> [-flip]
+ run-mummer1 Script to run alignment programs. Format is:
+ run-mummer1 <genome1> <genome2> <tag> [-flip]
<tag> will be used to make output files: <tag>.out , <tag>.gaps
and <tag>.align . -r will reverse complement <genome2>
--- a/docs/web/manual/index.html
+++ b/docs/web/manual/index.html
@@ -516,7 +516,6 @@ td {
<li><code>make (GNU make 3.79.1)</code></li>
<li><code>perl (PERL 5.6.0)</code></li>
<li><code>sh (GNU sh 1.14.7)</code></li>
- <li><code>csh (tcsh 6.10.00)</code></li>
<li><code>g++ (GNU gcc 2.95.3)</code></li>
<li><code>sed (GNU sed 3.02)</code></li>
<li><code>awk (GNU awk 3.0.4)</code></li>
@@ -647,7 +646,7 @@ td {
can also be viewed with the same utility programs (see above). Refer to the
<a href="#promer">PROmer</a> section for a list of options and output descriptions.</p>
<h5>run-mummer1 and run-mummer3</h5>
-<p><code>run-mummer1</code> and <code>run-mummer3</code> are cshell script pipelines
+<p><code>run-mummer1</code> and <code>run-mummer3</code> are shell script pipelines
for the general alignment of two sequences. They follow the same three steps
of NUCmer and PROmer, in that they match, cluster and extend, however they handle
any input sequence, not just nucleotide. This non-discrimination can be useful,
@@ -1192,7 +1191,7 @@ Long Exact Matches:
repeat positions are denoted by an <code>'r'</code> following the Start2 position,
and are relative to the forward strand of the sequence.</p>
<h4><a name="exact"></a>5.1.3. exact-tandems</h4>
-<p><code>exact-tandems</code> is a wrapper cshell script for the <code>repeat-match</code>
+<p><code>exact-tandems</code> is a wrapper shell script for the <code>repeat-match</code>
program. It provides a list of exact tandem repeats within a single input sequence.</p>
<h5>Command line syntax</h5>
<p><code>exact-tandems <sequence file> <min length></code></p>
@@ -1910,7 +1909,7 @@ PROMER
and the reverse strand of the query.</p>
<h5>Program options</h5>
<p>There are no available command line options for <code>run-mummer1</code>. Instead,
- the user must directly edit the <code>csh</code> script to alter the command
+ the user must directly edit the <code>sh</code> script to alter the command
line values passed to the individual pipeline programs. The only available tweak
is changing the minimum match length value for <code>mummer</code>, set with
the <code>-l</code> option within the script. Decreasing this value may increase
@@ -2008,7 +2007,7 @@ S: tagctgtcggggcgatcccctcggtagtga
requires hand editing the script.</p>
<h5>Program options</h5>
<p>There are no available command line options for <code>run-mummer3</code>. Instead,
- the user must directly edit the <code>csh</code> script to alter the command
+ the user must directly edit the <code>sh</code> script to alter the command
line values passed to the individual pipeline programs. Altering these parameters
is suggested for most applications, as the default values may not always produce
the best output. Parameter values may be added or changed for <code>mummer</code>,
|
