10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
#!/bin/bash -l
#SBATCH -p node
#SBATCH -A <projectID>
#SBATCH -n 16
#SBATCH -t 7-00:00:00
#SBATCH --mem=128GB
#SBATCH --mail-type=ALL... (1 Reply)
Discussion started by: @man
1 Replies
2. Shell Programming and Scripting
Hi All,
I have 100 folders with the first delimiter has a unique name i.e (123_hello and 575_hello) and each folder have atlist 1000 plus files with naming convention i.e (575_hello_1.iso ... 575_hello_1000.iso).
575_hello/575_hello_1.iso
575_hello/575_hello_2.iso
575_hello/575_hello_3.iso... (8 Replies)
Discussion started by: lxdorney
8 Replies
3. UNIX for Dummies Questions & Answers
Hi,
I have a directory with a lot of files like this:
a.bam
b.bam
c.bam
I like to rename these files based on a list where the name of the files in the first column will be replasced by the names in the second column. Here is my list which is a tab-delimited text file:
a x
b y
c ... (4 Replies)
Discussion started by: a_bahreini
4 Replies
4. Shell Programming and Scripting
Is better way to write the script loop through one by one "Old_File_1: & New_File_1:" to copy 100 files to /staging/test folder then re-name & gzip all those files? I wrote this code below and don't like that much. Thanks
I have a control_file under /tmp/test folder like below 100 files and... (10 Replies)
Discussion started by: dotran
10 Replies
5. Shell Programming and Scripting
I have a sourcefile which contains data as below.I want to check whether datatype,structure and date format looks good as mentioned.
Data is delemited by cydila Ç.
Source file-Emp.txt
snoÇnameÇphonenoÇdeptÇjoineddate
1ÇvivekÇ0861ÇCSEÇ2013-05-29 00:00:00
2ÇdineshÇ123456ÇECEÇ2013-05-29 00:00:00... (8 Replies)
Discussion started by: katakamvivek
8 Replies
6. Shell Programming and Scripting
How can i rename list of files in a directory? (4 Replies)
Discussion started by: knip
4 Replies
7. Shell Programming and Scripting
I am currently writing a script in AIX
I connected to the database using SQL *PLUS
I need to retrive data of Number of rows inserted today in the table(TABLE_NAME) which has column DATETIME(DDMMYYYY)
I tried using
select TO_CHAR(sysdate, 'DDMMYYYY') CHRDATE from dual
select count (*)... (2 Replies)
Discussion started by: PhAnT0M
2 Replies
8. Shell Programming and Scripting
Hi,
I need to do something easy but I can't seem to figure out how to do this.
Let's say I have 6 files in the directory below:
/ebsbeta_f/flash/EBSUATQB/onlinelog
o1_mf_6_55klt7nr_.log
o1_mf_3_55klskj4_.log
o1_mf_4_55klsrl1_.log
o1_mf_5_55klt09p_.log
o1_mf_2_55klv1ts_.log... (10 Replies)
Discussion started by: exm
10 Replies
9. Shell Programming and Scripting
Hi Friend,
I have a small script to list all file FFAAAAABBBBB00001 and FFAAAAABBBBB00001.repaired (when I run another script, the orginal file will output another *.repaired file) in my unix directory, and reaname the output file FFAAAAABBBBB00001.repaired back to FFAAAABBBBB00001. However, it... (2 Replies)
Discussion started by: happyv
2 Replies
10. UNIX for Dummies Questions & Answers
Hi all,
I am a newbie in writng unix..I am using ksh shell..Does anyone know how to copy a list o files from directory A to directory B with differnt names? i.e
in Dir A, I have
RPT101.555.TXT
RPT102.666.TXT
and I want to copy those files to dir B with new naming convention..
in Dir B,... (7 Replies)
Discussion started by: kinmak
7 Replies
BUNDLE-EXEC(1) BUNDLE-EXEC(1)
NAME
bundle-exec - Execute a command in the context of the bundle
SYNOPSIS
bundle exec command
DESCRIPTION
This command executes the command, making all gems specified in the Gemfile(5) available to require in Ruby programs.
Essentially, if you would normally have run something like rspec spec/my_spec.rb, and you want to use the gems specified in the Gemfile(5)
and installed via bundle install(1) bundle-install.1.html, you should run bundle exec rspec spec/my_spec.rb.
Note that bundle exec does not require that an executable is available on your shell's $PATH.
BUNDLE INSTALL --BINSTUBS
If you use the --binstubs flag in bundle install(1) bundle-install.1.html, Bundler will automatically create a directory (which defaults to
app_root/bin) containing all of the executables available from gems in the bundle.
After using --binstubs, bin/rspec spec/my_spec.rb is identical to bundle exec rspec spec/my_spec.rb.
ENVIRONMENT MODIFICATIONS
bundle exec makes a number of changes to the shell environment, then executes the command you specify in full.
o make sure that it's still possible to shell out to bundle from inside a command invoked by bundle exec (using $BUNDLE_BIN_PATH)
o put the directory containing executables (like rails, rspec, rackup) for your bundle on $PATH
o make sure that if bundler is invoked in the subshell, it uses the same Gemfile (by setting BUNDLE_GEMFILE)
o add -rbundler/setup to $RUBYOPT, which makes sure that Ruby programs invoked in the subshell can see the gems in the bundle
It also modifies Rubygems:
o disallow loading additional gems not in the bundle
o modify the gem method to be a no-op if a gem matching the requirements is in the bundle, and to raise a Gem::LoadError if it's not
o Define Gem.refresh to be a no-op, since the source index is always frozen when using bundler, and to prevent gems from the system leak-
ing into the environment
o Override Gem.bin_path to use the gems in the bundle, making system executables work
o Add all gems in the bundle into Gem.loaded_specs
Shelling out
When shelling out (using the system or backticks methods, for example), Bundler's environment changes will propagate to the subshell envi-
ronment. If you desire to shell out without Bundler's environment changes, simply employ the with_clean_env method. It will restore all
environment variables to what they were before Bundler was activated. For example:
Bundler.with_clean_env do
`brew install wget`
end
RUBYGEMS PLUGINS
At present, the Rubygems plugin system requires all files named rubygems_plugin.rb on the load path of any installed gem when any Ruby code
requires rubygems.rb. This includes executables installed into the system, like rails, rackup, and rspec.
Since Rubygems plugins can contain arbitrary Ruby code, they commonly end up activating themselves or their dependencies.
For instance, the gemcutter 0.5 gem depended on json_pure. If you had that version of gemcutter installed (even if you also had a newer
version without this problem), Rubygems would activate gemcutter 0.5 and json_pure <latest>.
If your Gemfile(5) also contained json_pure (or a gem with a dependency on json_pure), the latest version on your system might conflict
with the version in your Gemfile(5), or the snapshot version in your Gemfile.lock.
If this happens, bundler will say:
You have already activated json_pure 1.4.6 but your Gemfile
requires json_pure 1.4.3. Consider using bundle exec.
In this situation, you almost certainly want to remove the underlying gem with the problematic gem plugin. In general, the authors of these
plugins (in this case, the gemcutter gem) have released newer versions that are more careful in their plugins.
You can find a list of all the gems containing gem plugins by running
ruby -rubygems -e "puts Gem.find_files('rubygems_plugin.rb')"
At the very least, you should remove all but the newest version of each gem plugin, and also remove all gem plugins that you aren't using
(gem uninstall gem_name).
March 2013 BUNDLE-EXEC(1)