12.2. What are the dependencies¶
There are two kind of dependencies. First, the Python libraries such as matplotlib or Pandas. Second, the external tools such as BWA (alignment) or Kraken (taxonomy). The first kind of tools can be installed using Anaconda and the default conda channel. For instance:
conda install pandas
The second kind of tools can also be installed using another conda channel called bioconda. For instance:
conda install bwa
The full list of dependencies will be maintained in the Installation section but those two lines should be sufficient to install most of the dependencies with conda:
conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements.txt conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines.txt
Additional tools such as prokka, busco, canu and future heavy software will be maintained in this specific requirements for now:
conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines_extra.txt
12.3. Installation issues¶
As explained in the previous section, most of the dependencies can be installed via Conda. If not, pip is recommended. Yet there are still a few dependencies that needs manual installation.
wget https://downloads.sourceforge.net/project/quast/quast-4.2.tar.gz tar -xzf quast-4.2.tar.gz cd quast-4.2
Alternatively, get the source code from their GitHub (takes a while):
git clone https://github.com/ablab/quast cd quast python setup.py install
graphviz provides an executable called dot. If you type dot in a shell and get this error message:
Warning: Could not load ...lib/graphviz/libgvplugin_gd.so.6" - file not found
This may be solved by re-installation graphviz using the main anaconda channel (instead of bioconda):
conda install --override-channels -c anaconda graphviz=2.38.0
|Update April 2017:|
|replace anaconda with conda-forge|
If you get errors related to the X connection, you may need to change the backend of matplotlib. To do so, go in your home directory and in this directory
Check if the file matplotlibrc exits, if not, type:
echo "backend: Agg" > matplotlibrc
or edit the file and make sure the line starting with “backend” uses the Agg backend:
Save, exit the shell, start a new shell.
12.3.4. pysam / samtools / bzip2¶
We have experienced few issues with pysam and samtools. Here are some solutions.
from pysam.libchtslib import * ...ImportError: libhts.so.1: cannot open shared object file: No such file or directory
This may be solved by removing conda installation and using pip instead:
conda remove pysam pip install pysam
Another error know for pysam version 0.11.2.2 raises this error:
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory
Downgrading to version 0.11.2.1 and upgrading to working version solves the problem:
conda install pysam=0.11.2.1
but one reason was also related to the order of the channel in the .condarc file. You may get bzip2 from the default channel and not from conda-forge (reference: https://github.com/bioconda/bioconda-recipes/issues/5188)
conda install --override-channels -c conda-forge bzip2
from PyQt5.QtWebKitWidgets import QWebView ...ImportError: libQt5WebKitWidgets.so.5: cannot open shared object file: No such file or directory
This may be solved by re-installation qt using the main anaconda channel (instead of bioconda):
conda install --override-channels -c anaconda qt
12.4. Expected input format¶
Most of the pipelines and standalone expect FastQ files with the extension fastq.gz meaning that files are gzipped.
Besides, the filename convention is as follows:
that is _R1_ and _R2_ indicates the paired or single-ended files and the PREFIX is used to create directories or reports; it must be present.
New in version 0.2: more flexible tags are now possible in sequana pipelines and sequanix using e.g. _R in the input_readtag in the configuration file of the pipelines.
12.6. QXcbConnection issue¶
If you get this error:
QXcbConnection: Could not connect to display localhost:10.0
this is an issue with your Qt backend. You need to change it to Agg.
12.7. Variant Calling pipeline¶
If snpeff fails with this type of errors:
java.lang.RuntimeException: Error reading file 'null' java.lang.RuntimeException: Cannot find sequence for 'LN831026.gbk'
this may be because your genbank does not contain the sequences.
Another type of errors is that the sequence and genbank are not synchrone. We would recommend to use the code here to download the Fasta and genbank:
If you use the singularity container and get this kind of error:
singularity shell sequana-sequana-master.img ERROR : Base home directory does not exist within the container: /pasteur ABORT : Retval = 255
it means the container does not know about the Base home directory.
If you have sudo access, add the missing path as follows:
sudo singularity shell --writable sequana-sequana-master.img mkdir /pasteur exit
If you do not have sudo permissions, copy the image on a computer where you have such permission, use the same code as above and copy back the new image on the computer where you had the issue.
Finally, try to use the container again using this code:
singularity shell sequana-sequana-master.img