How to read a file into a variable in shell?

https://stackoverflow.com/questions/7427262/how-to-read-a-file-into-a-variable-in-shell


1. make file name list

ls | grep .gz > file_name_list.txt


2.  read file into shell variable & do 'for'

value=$(<file_name_list.txt)
for name in $value
do
/program_path/program -i /file_path/${name}
done

mount iso file in linux

https://askubuntu.com/questions/164227/how-to-mount-an-iso-file

1. Create a directory to serve as the mount location:
   

   sudo mkdir /mnt/iso
   

2. Mount the ISO in the target directory:
   

   sudo mount -o loop path/to/iso/file/YOUR_ISO_FILE.ISO /mnt/iso
   

3. Unmount the ISO:
   

   sudo umount /mnt/iso
   

tophat install error : except getopt.error, msg: SyntaxError: invalid syntax

http://seqanswers.com/forums/showthread.php?t=17514

Error :
File "./tophat", line 1003
    except getopt.error, msg:
                       ^
SyntaxError: invalid syntax

To solve :
edit tophat

#!/usr/bin/env python2

instead of

#!/usr/bin/env python


This error comes from the difference between python2 and python3.

check your path  and version of python

python - List Comprehensions

python - List Comprehensions

https://docs.python.org/2/tutorial/datastructures.html#list-comprehensions

List comprehensions provide a concise way to create lists. Common applications are to make new lists where each element is the result of some operations applied to each member of another sequence or iterable, or to create a subsequence of those elements that satisfy a certain condition.
For example, assume we want to create a list of squares, like:

>>> squares = []
>>> for x in range(10):
...     squares.append(x**2)
...
>>> squares
[0, 1, 4, 9, 16, 25, 36, 49, 64, 81]

We can obtain the same result with:

squares = [x**2 for x in range(10)]

This is also equivalent to squares = map(lambda x: x**2, range(10)), but it’s more concise and readable.
A list comprehension consists of brackets containing an expression followed by a for clause, then zero or more for or if clauses. The result will be a new list resulting from evaluating the expression in the context of the for and if clauses which follow it. For example, this listcomp combines the elements of two lists if they are not equal:

>>> [(x, y) for x in [1,2,3] for y in [3,1,4] if x != y]
[(1, 3), (1, 4), (2, 3), (2, 1), (2, 4), (3, 1), (3, 4)]

and it’s equivalent to:

>>> combs = []
>>> for x in [1,2,3]:
...     for y in [3,1,4]:
...         if x != y:
...             combs.append((x, y))
...
>>> combs
[(1, 3), (1, 4), (2, 3), (2, 1), (2, 4), (3, 1), (3, 4)]

How to access data in SRA

Good series of posts on how to access data in SRA

https://edwards.sdsu.edu/research/lab-blog/sra/

install R with --enable-R-shlib=yes [for shared library]

install R with --enable-R-shlib=yes  [for shared library]

if you have pre-installed R and want to install new version of R,

you need to install new version of R with shared library to share library with old version

and run rstudio.

https://stackoverflow.com/questions/28096239/how-to-configure-r-3-1-2-with-enable-r-shlib

Qt: XKEYBOARD extension not present on the X server.

check details in
https://github.com/spyder-ide/spyder/issues/3713


From replies

athlonshi commented on 4 Jul 2017

For those using Exceed X Server, you may also need to change Xconfig setting. Go to Xconfig --> Settings --> Protocol... --> Extensions --> check XKEYBOARD and save the settings.

Oreki47 commented on 6 Oct 2017

I'm using TightVNC with Ubuntu 14.04.
It works on my machine with:
export XKB_DEFAULT_RULES=base
export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb
The set rules has to come first.