[med-svn] [spades] 01/03: New upstream version 3.9.1+dfsg
Sascha Steinbiss
satta at debian.org
Wed Dec 7 06:50:01 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository spades.
commit fb140eb70b3eebb2abed128ff58396eafbd8ccaa
Author: Sascha Steinbiss <satta at debian.org>
Date: Wed Dec 7 06:28:34 2016 +0000
New upstream version 3.9.1+dfsg
---
LICENSE | 6 ++---
README | 2 +-
VERSION | 2 +-
changelog.html | 6 ++++-
dipspades_manual.html | 4 +--
manual.html | 52 ++++++++++++++++++------------------
rnaspades_manual.html | 6 ++---
src/cmake/pack.cmake | 6 ++---
src/projects/hammer/kmer_data.cpp | 28 ++++++++++++++++---
src/projects/mph_test/CMakeLists.txt | 4 +++
src/spades_pipeline/support.py | 6 ++---
truspades_manual.html | 2 +-
12 files changed, 76 insertions(+), 48 deletions(-)
diff --git a/LICENSE b/LICENSE
index 27b20f9..9decf09 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,5 +1,5 @@
SPADES: SAINT-PETERSBURG GENOME ASSEMBLER
-Copyright (c) 2015 Saint Petersburg State University
+Copyright (c) 2015-2016 Saint Petersburg State University
Copyright (c) 2011-2014 Saint Petersburg Academic University
SPAdes is free software; you can redistribute it and/or modify
@@ -49,8 +49,8 @@ Also contributed:
Nikolay Vyahhi
Contacts:
- http://bioinf.spbau.ru/spades
- spades.support at bioinf.spbau.ru
+ http://cab.spbu.ru/software/spades/
+ spades.support at cab.spbu.ru
References:
diff --git a/README b/README
index 742fb6c..3e67cc3 100755
--- a/README
+++ b/README
@@ -37,7 +37,7 @@ Also contributed:
Nikolay Vyahhi
Installation instructions and manual can be found on the website:
-http://bioinf.spbau.ru/spades
+http://cab.spbu.ru/software/spades/
References:
diff --git a/VERSION b/VERSION
index a5c4c76..6bd1074 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.9.0
+3.9.1
diff --git a/changelog.html b/changelog.html
index a60139f..6731f56 100644
--- a/changelog.html
+++ b/changelog.html
@@ -3,6 +3,10 @@
<h2>SPAdes Genome Assembler changelog</h2>
+<h3>SPAdes 3.9.1, 4 December 2016</h3>
+
+<p>FIX: macOS Sierra crash.</p>
+
<h3>SPAdes 3.9.0, 23 July 2016</h3>
<p>NEW: rnaSPAdes pipeline for de novo transcriptome assembly from RNA-Seq data.</p>
@@ -215,7 +219,7 @@
<p>Initial release.</p>
<p>
- <a href="http://bioinf.spbau.ru/en/spades">SPAdes site</a>
+ <a href="http://cab.spbu.ru/software/spades/">SPAdes website</a>
</p>
</body>
diff --git a/dipspades_manual.html b/dipspades_manual.html
index ff3b7dd..f480ae0 100644
--- a/dipspades_manual.html
+++ b/dipspades_manual.html
@@ -230,14 +230,14 @@ Names correspond to the names of haplocontigs specified as an input using option
<p>
If you use dipSPAdes in your research, please include <a href="http://link.springer.com/chapter/10.1007/978-3-319-05269-4_21" target="_blank">Safonova, Bankevich, and Pevzner, 2014</a> in your reference list.
<p>
- In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+ In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to <a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
<br>
<a id = "feedback"></a>
<h2>5. Feedback and bug reports</h2>
Your comments, bug reports, and suggestions are very welcomed. <br>
If you have trouble running dipSPAdes, please provide us with the files params.txt and dipspades.log from the directory <output_dir>. <br>
-Address for communications: <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+Address for communications: <<a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
</body>
</html>
diff --git a/manual.html b/manual.html
index b389735..6b02feb 100644
--- a/manual.html
+++ b/manual.html
@@ -1,6 +1,6 @@
<html>
<head>
- <title>SPAdes 3.9.0 Manual</title>
+ <title>SPAdes 3.9.1 Manual</title>
<style type="text/css">
.code {
background-color: lightgray;
@@ -8,7 +8,7 @@
</style>
</head>
<body>
-<h1>SPAdes 3.9.0 Manual</h1>
+<h1>SPAdes 3.9.1 Manual</h1>
1. <a href="#sec1">About SPAdes</a><br>
1.1. <a href="#sec1.1">Supported data types</a><br>
@@ -35,16 +35,16 @@
<h2>1. About SPAdes</h2>
<p>
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes.
-SPAdes version 3.9.0 was released under GPLv2 on July 23, 2016 and can be downloaded from <a href="http://bioinf.spbau.ru/en/spades" target="_blank">http://bioinf.spbau.ru/en/spades</a>.
+SPAdes version 3.9.1 was released under GPLv2 on December 4, 2016 and can be downloaded from <a href="http://cab.spbu.ru/software/spades/" target="_blank">http://cab.spbu.ru/software/spades/</a>.
<a name="sec1.1"></a>
<h3>1.1 Supported data types</h3>
<p>
The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.
<p>
- Version 3.9.0 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.
+ Version 3.9.1 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.
<p>
- SPAdes 3.9.0 includes the following additional pipelines:
+ SPAdes 3.9.1 includes the following additional pipelines:
<ul>
<li>dipSPAdes – a module for assembling highly polymorphic diploid genomes (see <a href="dipspades_manual.html" target="_blank">dipSPAdes manual</a>).</li>
<li>metaSPAdes – a pipeline for metagenomic data sets (see <a href="#meta">metaSPAdes options</a>). </li>
@@ -143,7 +143,7 @@ SPAdes comes in several separate modules:
<li> Running SPAdes without preliminary read error correction (e.g. without BayesHammer or IonHammer) will likely require more time and memory. </li>
<li> Each module removes its temporary files as soon as it finishes. </li>
<li> SPAdes uses 512 Mb per thread for buffers, which results in higher memory consumption. If you set memory limit manually, SPAdes will use smaller buffers and thus less RAM. </li>
- <li> Performance statistics is given for SPAdes version 3.9.0. </li>
+ <li> Performance statistics is given for SPAdes version 3.9.1. </li>
</ul>
@@ -157,13 +157,13 @@ SPAdes comes in several separate modules:
<h3>2.1 Downloading SPAdes Linux binaries</h3>
<p>
- To download <a href="http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz">SPAdes Linux binaries</a> and extract them, go to the directory in which you wish SPAdes to be installed and run:
+ To download <a href="http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Linux.tar.gz">SPAdes Linux binaries</a> and extract them, go to the directory in which you wish SPAdes to be installed and run:
<pre class="code">
<code>
- wget http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz
- tar -xzf SPAdes-3.9.0-Linux.tar.gz
- cd SPAdes-3.9.0-Linux/bin/
+ wget http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Linux.tar.gz
+ tar -xzf SPAdes-3.9.1-Linux.tar.gz
+ cd SPAdes-3.9.1-Linux/bin/
</code>
</pre>
@@ -192,13 +192,13 @@ SPAdes comes in several separate modules:
<h3>2.2 Downloading SPAdes binaries for Mac</h3>
<p>
- To obtain <a href="http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Darwin.tar.gz">SPAdes binaries for Mac</a>, go to the directory in which you wish SPAdes to be installed and run:
+ To obtain <a href="http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Darwin.tar.gz">SPAdes binaries for Mac</a>, go to the directory in which you wish SPAdes to be installed and run:
<pre class="code">
<code>
- curl http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Darwin.tar.gz -o SPAdes-3.9.0-Darwin.tar.gz
- tar -zxf SPAdes-3.9.0-Darwin.tar.gz
- cd SPAdes-3.9.0-Darwin/bin/
+ curl http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Darwin.tar.gz -o SPAdes-3.9.1-Darwin.tar.gz
+ tar -zxf SPAdes-3.9.1-Darwin.tar.gz
+ cd SPAdes-3.9.1-Darwin/bin/
</code>
</pre>
@@ -236,13 +236,13 @@ SPAdes comes in several separate modules:
</ul>
<p>
- If you meet these requirements, you can download the <a href="http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0.tar.gz">SPAdes source code</a>:
+ If you meet these requirements, you can download the <a href="http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1.tar.gz">SPAdes source code</a>:
<pre class="code">
<code>
- wget http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0.tar.gz
- tar -xzf SPAdes-3.9.0.tar.gz
- cd SPAdes-3.9.0
+ wget http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1.tar.gz
+ tar -xzf SPAdes-3.9.1.tar.gz
+ cd SPAdes-3.9.1
</code>
</pre>
@@ -349,7 +349,7 @@ Thank you for using SPAdes!
SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.
<p>
- To run SPAdes 3.9.0 you need at least one library of the following types:
+ To run SPAdes 3.9.1 you need at least one library of the following types:
<ul>
<li>Illumina paired-end/high-quality mate-pairs/unpaired reads</li>
<li>IonTorrent paired-end/high-quality mate-pairs/unpaired reads</li>
@@ -522,7 +522,7 @@ Note that we assume that SPAdes installation directory is added to the <code>PAT
<a name="correctoropt">
<p>
<code>--careful</code><br>
- Tries to reduce the number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses <a href="http://bio-bwa.sourceforge.net" target="_blank">BWA</a> tool (comes with SPAdes). This option is recommended for single-genome assembly, but is not supported by metaSPAdes metagenomic pipeline.
+ Tries to reduce the number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses <a href="http://bio-bwa.sourceforge.net" target="_blank">BWA</a> tool (comes with SPAdes). This option is recommended only for assembly of small genomes. We strongly recommend not to use it for large and medium-size eukaryotic genomes. Note, that this options is is not supported by metaSPAdes and rnaSPAdes.
</p>
@@ -1096,8 +1096,8 @@ However, it might be tricky to fully utilize the advantages of long reads you h
<ul>
<li><code><output_dir>/corrected/</code> directory contains reads corrected by BayesHammer in <code>*.fastq.gz</code> files; if compression is disabled, reads are stored in uncompressed <code>*.fastq</code> files</li>
+ <li><code><output_dir>/scaffolds.fasta</code> contains resulting scaffolds (recommended for use as resulting sequences)</li>
<li><code><output_dir>/contigs.fasta</code> contains resulting contigs</li>
- <li><code><output_dir>/scaffolds.fasta</code> contains resulting scaffolds</li>
<li><code><output_dir>/assembly_graph.fastg</code> contains SPAdes assembly graph in <a href="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf" target="_blank">FASTG format</a></li>
<li><code><output_dir>/contigs.paths</code> contains paths in the assembly graph corresponding to contigs.fasta (see details below)</li>
<li><code><output_dir>/scaffolds.paths</code> contains paths in the assembly graph corresponding to scaffolds.fasta (see details below)</li>
@@ -1143,8 +1143,8 @@ states that <code>NODE_3_length_237403_cov_243.207_ID_45</code> corresponds to t
The full list of <code><output_dir></code> content is presented below:
</p>
<pre>
+ <code>scaffolds.fasta</code> – <i>resulting scaffolds (recommended for use as resulting sequences)</i>
<code>contigs.fasta</code> – <i>resulting contigs</i>
- <code>scaffolds.fasta</code> – <i>resulting scaffolds </i>
<code>assembly_graph.fastg</code> – <i>assembly graph</i>
<code>contigs.paths</code> – <i>contigs paths in the assembly graph</i>
<code>scaffolds.paths</code> – <i>scaffolds paths in the assembly graph</i>
@@ -1159,7 +1159,7 @@ The full list of <code><output_dir></code> content is presented below:
<code>spades.log</code> – <i>SPAdes log</i>
<code>dataset.info</code> – <i>internal configuration file</i>
<code>input_dataset.yaml</code> – <i>internal YAML data set file</i>
- <code>K<##>/</code> – <i>directory containing files from the run with K=<##> </i>
+ <code>K<##>/</code> – <i>directory containing intermediate files from the run with K=<##>. These files should not be used as assembly results; use resulting contigs/scaffolds in files mentioned above.</i>
</pre>
<p>
@@ -1176,7 +1176,7 @@ we append suffix <code>_component_X</code>, where <code>X</code> is the id of th
<p>
- <a href="http://bioinf.spbau.ru/en/quast" target="_blank">QUAST</a> may be used to generate summary statistics (N50, maximum contig length, GC %, # genes found in a reference list or with built-in gene finding tools, etc.) for a single assembly. It may also be used to compare statistics for multiple assemblies of the same data set (e.g., SPAdes run with different parameters, or several different assemblers).
+ <a href="http://cab.spbu.ru/software/quast/" target="_blank">QUAST</a> may be used to generate summary statistics (N50, maximum contig length, GC %, # genes found in a reference list or with built-in gene finding tools, etc.) for a single assembly. It may also be used to compare statistics for multiple assemblies of the same data set (e.g., SPAdes run with different parameters, or several different assemblers).
<br>
@@ -1193,7 +1193,7 @@ we append suffix <code>_component_X</code>, where <code>X</code> is the id of th
For the information about dipSPAdes and truSPAdes papers see <a href="dipspades_manual.html" target="_blank">dipSPAdes manual</a> and <a href="truspades_manual.html" target="_blank">truSPAdes manual</a> respectively.
<p>
- In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+ In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to <a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
<br>
@@ -1206,7 +1206,7 @@ we append suffix <code>_component_X</code>, where <code>X</code> is the id of th
If you have any troubles running SPAdes, please send us <code>params.txt</code> and <code>spades.log</code> from the directory <code><output_dir></code>.
<p>
- Address for communications: <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+ Address for communications: <a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
<br/><br/><br/><br/><br/>
diff --git a/rnaspades_manual.html b/rnaspades_manual.html
index a072965..7b5199b 100644
--- a/rnaspades_manual.html
+++ b/rnaspades_manual.html
@@ -19,7 +19,7 @@
<a name="sec1"></a>
<h2>1 About rnaSPAdes</h2>
-<p> rnaSPAdes is a tool for <i>de novo</i> transcriptome assembly from RNA-Seq data and is suitable for all kind of organisms. rnaSPAdes is a part of <a href="http://bioinf.spbau.ru/en/spades">SPAdes package</a> since version 3.9. Information about SPAdes download, requirements, installation and basic options can be found in <a href="manual.html">SPAdes manual</a>. Below you may find information about differences between SPAdes and rnaSPAdes.
+<p> rnaSPAdes is a tool for <i>de novo</i> transcriptome assembly from RNA-Seq data and is suitable for all kind of organisms. rnaSPAdes is a part of <a href="http://cab.spbu.ru/software/spades/">SPAdes package</a> since version 3.9. Information about SPAdes download, requirements, installation and basic options can be found in <a href="manual.html">SPAdes manual</a>. Below you may find information about differences between SPAdes and rnaSPAdes.
<a name="sec2"></a>
<h2>2 rnaSPAdes specifics</h2>
@@ -58,7 +58,7 @@ Note that we assume that SPAdes installation directory is added to the <code>PAT
<h2>3 Assembly evaluation</h2>
<p>
- <a href="http://bioinf.spbau.ru/en/rnaquast" target="_blank">rnaQUAST</a> may be used for transcriptome assembly quality assessment for model organisms when reference genome and gene database are available. rnaQUAST also includes <a href="http://busco.ezlab.org/" target="_blank">BUSCO</a> and <a href="http://topaz.gatech.edu/GeneMark/" target="_blank"> GeneMarkS-T</a> tools for <i>de novo</i> evaluation.
+ <a href="http://cab.spbu.ru/software/rnaquast/" target="_blank">rnaQUAST</a> may be used for transcriptome assembly quality assessment for model organisms when reference genome and gene database are available. rnaQUAST also includes <a href="http://busco.ezlab.org/" target="_blank">BUSCO</a> and <a href="http://topaz.gatech.edu/GeneMark/" target="_blank"> GeneMarkS-T</a> tools for <i>de novo</i> evaluation.
<br>
<a name="sec4">
@@ -76,7 +76,7 @@ If you use rnaSPAdes in your research, please include main SPAdes paper <a href=
If you have any troubles running rnaSPAdes, please send us <code>params.txt</code> and <code>spades.log</code> from the directory <code><output_dir></code>.
<p>
- Address for communications: <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+ Address for communications: <a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
<br/><br/><br/><br/><br/>
diff --git a/src/cmake/pack.cmake b/src/cmake/pack.cmake
index 318c2d0..b5982c0 100644
--- a/src/cmake/pack.cmake
+++ b/src/cmake/pack.cmake
@@ -9,13 +9,13 @@ else()
endif()
set(CPACK_PACKAGE_NAME "SPAdes")
-set(CPACK_PACKAGE_VENDOR "Saint Petersburg Academic University")
+set(CPACK_PACKAGE_VENDOR "Saint Petersburg State University")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${SPADES_MAIN_SRC_DIR}/../README")
set(CPACK_RESOURCE_FILE_LICENSE "${SPADES_MAIN_SRC_DIR}/../LICENSE")
-set(CPACK_PACKAGE_VERSION "3.9.0")
+set(CPACK_PACKAGE_VERSION "3.9.1")
set(CPACK_PACKAGE_VERSION_MAJOR "3")
set(CPACK_PACKAGE_VERSION_MINOR "9")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
+set(CPACK_PACKAGE_VERSION_PATCH "1")
set(CPACK_STRIP_FILES bin/spades bin/hammer bin/ionhammer bin/dipspades bin/spades-bwa bin/corrector bin/scaffold_correction)
# Source stuff
diff --git a/src/projects/hammer/kmer_data.cpp b/src/projects/hammer/kmer_data.cpp
index 16d1128..22b2aac 100644
--- a/src/projects/hammer/kmer_data.cpp
+++ b/src/projects/hammer/kmer_data.cpp
@@ -60,10 +60,16 @@ class BufferFiller {
: splitter_(splitter) {}
bool operator()(std::unique_ptr<Read> r) {
- uint8_t trim_quality = (uint8_t)cfg::get().input_trim_quality;
+ int trim_quality = cfg::get().input_trim_quality;
+ Read cr = *r;
+ size_t sz = cr.trimNsAndBadQuality(trim_quality);
+
+ if (sz < hammer::K)
+ return false;
+
unsigned thread_id = omp_get_thread_num();
- ValidKMerGenerator<hammer::K> gen(*r, trim_quality);
+ ValidKMerGenerator<hammer::K> gen(cr);
bool stop = false;
for (; gen.HasMore(); gen.Next()) {
KMer seq = gen.kmer();
@@ -192,7 +198,14 @@ class KMerMultiplicityCounter {
bool operator()(std::unique_ptr<Read> r) {
uint8_t trim_quality = (uint8_t)cfg::get().input_trim_quality;
- ValidKMerGenerator<hammer::K> gen(*r, trim_quality);
+ // FIXME: Get rid of this
+ Read cr = *r;
+ size_t sz = cr.trimNsAndBadQuality(trim_quality);
+
+ if (sz < hammer::K)
+ return false;
+
+ ValidKMerGenerator<hammer::K> gen(cr);
for (; gen.HasMore(); gen.Next()) {
KMer kmer = gen.kmer();
@@ -223,7 +236,14 @@ class KMerCountEstimator {
bool operator()(std::unique_ptr<Read> r) {
uint8_t trim_quality = (uint8_t)cfg::get().input_trim_quality;
- ValidKMerGenerator<hammer::K> gen(*r, trim_quality);
+ // FIXME: Get rid of this
+ Read cr = *r;
+ size_t sz = cr.trimNsAndBadQuality(trim_quality);
+
+ if (sz < hammer::K)
+ return false;
+
+ ValidKMerGenerator<hammer::K> gen(cr);
for (; gen.HasMore(); gen.Next()) {
KMer kmer = gen.kmer();
auto &hll = hll_[omp_get_thread_num()];
diff --git a/src/projects/mph_test/CMakeLists.txt b/src/projects/mph_test/CMakeLists.txt
index 0d0a3d8..7338861 100644
--- a/src/projects/mph_test/CMakeLists.txt
+++ b/src/projects/mph_test/CMakeLists.txt
@@ -13,3 +13,7 @@ add_executable(spades-kmercount
main.cpp)
target_link_libraries(spades-kmercount spades_modules ${COMMON_LIBRARIES})
+
+if (SPADES_STATIC_BUILD)
+ set_target_properties(spades-kmercount PROPERTIES LINK_SEARCH_END_STATIC 1)
+endif()
diff --git a/src/spades_pipeline/support.py b/src/spades_pipeline/support.py
index da7e65a..2df2199 100644
--- a/src/spades_pipeline/support.py
+++ b/src/spades_pipeline/support.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
############################################################################
-# Copyright (c) 2015 Saint Petersburg State University
+# Copyright (c) 2015-2016 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
@@ -39,11 +39,11 @@ def error(err_str, log=None, dipspades=False, prefix=SPADES_PY_ERROR_MESSAGE):
if log:
log.info("\n\n" + prefix + " " + err_str)
log_warnings(log, with_error=True)
- log.info("\nIn case you have troubles running " + binary_name + ", you can write to spades.support at bioinf.spbau.ru")
+ log.info("\nIn case you have troubles running " + binary_name + ", you can write to spades.support at cab.spbu.ru")
log.info("Please provide us with params.txt and " + binary_name.lower() + ".log files from the output directory.")
else:
sys.stderr.write("\n\n" + prefix + " " + err_str + "\n\n")
- sys.stderr.write("\nIn case you have troubles running " + binary_name + ", you can write to spades.support at bioinf.spbau.ru\n")
+ sys.stderr.write("\nIn case you have troubles running " + binary_name + ", you can write to spades.support at cab.spbu.ru\n")
sys.stderr.write("Please provide us with params.txt and " + binary_name.lower() + ".log files from the output directory.\n")
sys.stderr.flush()
if current_tmp_dir and os.path.isdir(current_tmp_dir):
diff --git a/truspades_manual.html b/truspades_manual.html
index ac2bc51..8a7dbc0 100644
--- a/truspades_manual.html
+++ b/truspades_manual.html
@@ -212,7 +212,7 @@ Note that we assume that truSPAdes installation directory is added to the <code>
If you have any troubles running truSPAdes, please send us <code>dataset.info</code> and <code>truspades.log</code> from the directory <code><output_dir></code>.
<p>
- Address for communications: <a href="mailto:spades.support at bioinf.spbau.ru" target="_blank">spades.support at bioinf.spbau.ru</a>.
+ Address for communications: <a href="mailto:spades.support at cab.spbu.ru" target="_blank">spades.support at cab.spbu.ru</a>.
<br/><br/><br/><br/><br/>
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