Using docker for application development

I found Docker super useful, but going through a manual is quite time consuming. Here, very stripped manual to create your first image and push it online 🙂

[bash]
# install docker
wget -qO- https://get.docker.com/ | sh

# add your user to docker group
sudo usermod -aG docker $USER

# check if it’s working
docker run docker/whalesay cowsay "hello world!"

# create an account on https://hub.docker.com
# and login
docker login -u $USER –email=EMAIL

# run image
docker run -it ubuntu

# make some changes ie. create user, install needed software etc

# finally open new terminal & commit changes (SESSIONID=HOSTNAME)
docker commit SESSIONID $USER/image:version

# mount local directory `pwd`/test as /test in read/write mode
docker run -it -v `pwd`/test:/test:rw $USER/image:version some command with arguments

# push image
docker push $USER/image:version
[/bash]

From now, you can get your image from any other machine connected to Internet by executing:
[bash]
docker run -it $USER/image:version
# ie. redundans image
docker run -it -w /root/src/redundans lpryszcz/redundans:v0.11b ./redundans.py -v -i test/{600,5000}_{1,2}.fq.gz -f test/contigs.fa -o test/run1

# you can create alias latest, then version can be skipped on running
docker tag lpryszcz/redundans:v0.11b lpryszcz/redundans:latest
docker push lpryszcz/redundans:latest

docker run -it lpryszcz/redundans
[/bash]

You can add info about your repository at https://hub.docker.com/r/$USER/image/

Working efficiently with millions of files

Working with millions of intermediate files can be very challenging, especially if you need to store them in distributed / network file system (NFS). This will make listing / navigating the directories to take ages… and removing of these files very time-consuming.
During building metaPhOrs DB, I needed to store some ~7.5 million of intermediate files that were subsequently processed in HPC. Saving these amount of files in the NFS would seriously affect not only myself, but also overall system performance.
One could store files in an archive, but then if you want to retrieve the data you would need to parse rather huge archives (tens-to-hundreds of GB) in order to retrieve rather small portions of data.
I have realised that TAR archives are natively supported in Python and can be indexed (see `tar_indexer`), which provide easy integration into existing code and random-access. If you work with text data, you can even zlib.compress the data stored inside you archives!
Below, I’m providing relevant parts of my code:
BASH
[bash]
# index content of multiple tar archives
tar2index.py -v -i db_*/*.tar -d archives.db3

# search for some_file in mutliple archives
tar2index.py -v -f some_file -d archives.db3
[/bash]

Python
[python]
import sqlite3, time
import tarfile, zlib, cStringIO

###
# lookup function
def tar_lookup(dbpath, file_name):
"""Return file name inside tar, tar file name, offset and file size."""
cur = sqlite3.connect(dbpath).cursor()
cur.execute("""SELECT o.file_name, f.file_name, offset, file_size
FROM offset_data as o JOIN file_data as f ON o.file_id=f.file_id
WHERE o.file_name like ?""", (file_name,))
return cur.fetchall()

###
# saving to archive
# open tarfile
tar = tarfile.open(tarpath, "w")
# save files to tar
for fname, txt in files_generator:
# compress file content (optionally)
gztxt = zlib.compress(txt)
# get tarinfo
ti = tarfile.TarInfo(fname)
ti.size = len(gztxt)
ti.mtime = time.time()
# add to tar
tar.addfile(ti, cStringIO.StringIO(gztxt))

###
# reading from indexed archive(s)
# NOTE: before you need to run tar2index.py on your archives
tarfnames = tar_lookup(index_path, file_name)
for i, (name, tarfn, offset, file_size) in enumerate(tarfnames, 1):
tarf = open(tarfn)
# move pointer to right archive place
tarf.seek(offset)
# read tar fragment & uncompress
txt = zlib.decompress(tarf.read(file_size))
[/python]

Conflicting config for htop on machines sharing same /home directory

My friend spotted a problem with htop configuration. Simply when htop was executed on two different Ubuntu distros (10.04 and 14.04) the config was reset.
After some interrogation, we have spotted that 10.04 stores htop config to ~/.htoprc, while 14.04 to ~/.config/htop/htoprc. It was enough to remove one of them and link another one as below:
[bash]
rm .htoprc
ln -s .config/htop/htoprc .htoprc
[/bash]

Connecting to MySQL without passwd prompt

If you are (like me) annoyed by providing password at every mysql login, you can skip it. Also it makes easier programmatic access to any MySQL db, as not passwd prompting is necessary 🙂
Create `~/.my.cnf` file:

[bash]
[client]
user=username
password="pass"

[mysql]
user=username
password="pass"
[/bash]

And login without `-p` parameter:
[bash]
mysql -h host -u username dbname
[/bash]

If you want to use `~/.my.cnf` file in MySQLdb, just connect using this:
[python]
import MySQLdb
cnx = MySQLdb.connect(host=host, port=port, read_default_file="~/.my.cnf")
[/python]

Batch convert of .xlsx (Microsoft Office) to .tsv (tab-delimited) files

I had to retrieve data from multiple .xlsx files with multiple sheets. This can be done manually, but it will be rather time-consuming tasks, plus Office quotes text fields, which is not very convenient for downstream analysis…
I have found handy script, xlsx2tsv.py, that does the job, but it reports only one sheet at the time. Thus, I have rewritten xlsx2tsv.py a little to save all sheets from given .xlsx file into separate folder. In addition, multiple .xlsx files can be process at once. My version can be found on github.
[bash]
xlsx2tsv.py *.xlsx
[/bash]

Pushing to multiple github repositories

Today I’ve faced problem with syncing two github repositories. Yes, I know, I shouldn’t keep two, but sometimes it’s difficult to avoid. Anyway, the problem is super easy to solve. It’s enough to edit `.git/config` by adding new remote:
[bash]
[remote "Origin"]
url = git@github.com:user1/repo1.git
url = git@github.com:user2/repo2.git
[/bash]

Of course, more than two repos can be added. Then, after next push all repositories will be synced.
[bash]
git push Origin master

Everything up-to-date

Counting objects: 61, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (61/61), done.
Writing objects: 100% (61/61), 5.73 KiB | 0 bytes/s, done.
Total 61 (delta 41), reused 0 (delta 0)
To git@github.com:user2/repo2.git
8b97528..8aed8c2 master -> master
[/bash]

Inspired by ruiabreu.

Easy citation in LibreOffice / OpenOffice with Mendeley

Creating reference list is always a nightmare. Mendeley and its handy LibreOffice / OpenOffice plugin may be of great help to many. It was for me. Below, I’ll describe how to make it working.
[bash]
# get & install mendeley from https://www.mendeley.com/download-mendeley-desktop/

# check version of your mendeley
# Help > About Mendeley Desktop

# clone repo and build plugin
git clone git@github.com:Mendeley/openoffice-plugin.git
cd openoffice-plugin/
python build.py 1.15.2 false

# add to LibreOffice
# Tools > Extension Manager > Add…
# and look for `Mendeley-1.15.2.oxt`
[/bash]

After OpenOffice / LibreOffice restart, you should see new bar. Note, in order for the plugin to work, Mendeley has to be running.

What’s great about this plugin, you can adjust citation style by just a few clicks by clicking on `Choose Citation Style`. There is quite extensive database of predefined citation styles, so adjusting the reference style to your favourite journal will take just a few seconds 🙂
More info about the plugin on github.