My goal is to use bcftools to check that the reference alleles in my dataset (vcf file) match with a reference genome (fasta file) using the fixref plugin.
Working on command line, I first set the following environment:
export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
The following code is recommended for test datasets with mismatches:
bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m top
When I run this code using my own files (please note that my data is .vcf, not .bcf) I get the following error:
[main] Unrecognized command
If I simply enter:
bcftools
I get a list of the only 5 commands (view, index, cat, ld, ldpair) that I can use. So although I've set the environment, does it somehow need to be activated? Do I need to run my command through a bash script?
bcftools
was pointing to a deprecated version of bcftools (0.1.19) in ../bin/, while
BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
was pointing to the plugins for bcftools version 1.10.2 outside /bin/
Replacing ../bin/bcftools (0.1.19 with 1.10.2) was the fix.
I have installed through Mainteinance Tool Qt 5.12.5 and the sources. I have the next directories:
C:\Qt\5.12.5\Src
C:\Qt\Tools\mingw730_32\
C:\Qt\Tools\mingw730_64\
On the other hand, I have read that downloable Postgres version is compiled with MSVC, and I must to compile my own version. I have do it following link, and now I have a postgresql version in c:\pgsql
Finally I have added c:\pgsql to user Path
Next step, I have opened PowerShell in Admin mode and I´ve gone to C:\Qt\5.12.5\Src\.
Next, set the env path for this PowerShell session:
$env:Path += ";C:\Qt\Tools\mingw730_64\bin\;C:\Qt\5.12.5\Src;C:\pgsql\include\;C:\pgsql\lib\;C:\pgsql\bin\" (setting the pgsql path again....)
After that, I execute configure.bat like that:
configure -v -static -release -static-runtime -platform win32-g++ -prefix C:\Qt\5.12.5\Estatico\ -opensource -confirm-license -qt-zlib -qt-pcre -qt-libpng -qt-libjpeg -qt-freetype -opengl desktop -no-openssl -opensource -confirm-license -skip webengine -make libs -nomake tools -nomake examples -nomake tests -sql-psql
But I have get this error:
ERROR: Feature 'sql-psql' was enabled, but the pre-condition 'libs.psql' failed.
Searching in config.log I can read those lines:
loaded result for library config.qtbase_sqldrivers.libraries.psql
Trying source 0 (type pkgConfig) of library psql ...
pkg-config use disabled globally.
=> source produced no result.
Trying source 1 (type psqlConfig) of library psql ...
pg_config not found.
=> source produced no result.
Trying source 2 (type psqlEnv) of library psql ...
None of [liblibpq.dll.a liblibpq.a libpq.dll.a libpq.a libpq.lib] found in [] and global paths.
=> source produced no result.
Trying source 3 (type psqlEnv) of library psql ...
=> source failed condition '!config.win32'.
test config.qtbase_sqldrivers.libraries.psql FAILED
What can I do or what is the properly way to do that?
Thank you in advance.
UPDATE
There are similar question here but it hasn´t been solved, and those question ask about Visual Studio.
I want to compile it under mingw.
The solution suggested by #Soheil Armin doesn´t work too
The solution suggested by #Soheil Armin works fine, but I need to delete the entire source tree and reinstall it as he suggested. If not, a new configure won't work.
Also, the ^ character can be saved:
configure <your parameters>
PSQL_LIBS="C:\pgsql\lib\libpq.a"
-I "C:\pgsql\include"
-L "C:\pgsql\lib"
You need to explicitly define library paths of Postgres.
configure <your parameters> ^
PSQL_LIBS="C:\pgsql\lib\libpq.a" ^
-I "C:\pgsql\include" ^
-L "C:\pgsql\lib"
Here the project structure cloned from github after compiling on Ubuntu successfully,
javaml
bin
net/sf/javaml/core/Dataset.class
javaml
src
net/sf/javaml/core/Dataset.java
When the following command wa given:
java -ea -classpath /home/shahid/git/javaml/bin:/home/shahid/a_f_w/randoop-3.1.5/randoop-all-3.1.5.jar randoop.main.Main gentests --testclass=net.sf.javaml.core.Dataset --literals-file=CLASSES
It generated the error: "Ignoring interface net.sf.javaml.core.Dataset specified via --classlist or --testclass.
No classes to test
".
while the other command java -ea -classpath /home/shahid/git/java-ml/bin:/home/shahid/a_f_w/randoop-3.1.5/randoop-all-3.1.5.jar randoop.main.Main gentests --testclass=DataSet --literals-file=CLASSESwithout package for other project working perfectly.
Any help will be appretiated.
The error message gives you the answer:
Ignoring interface net.sf.javaml.core.Dataset specified via --classlist or --testclass. No classes to test
You are supposed to provide a class, not an interface, to the --testclass command-line argument.
By passing --testclass=net.sf.javaml.core.Dataset to Randoop, you indicated that you only want Randoop to create objects of type net.sf.javaml.core.Dataset. However, since that is an interface, it cannot be instantiated, and Randoop cannot create any objects, nor any tests.
The following command worked for me:
java -ea -classpath ~/javaml/bin/:~/Randoop/randoop-all-3.1.4.jar randoop.main.Main gentests --testclass=net.sf.javaml.core.Complex --literals-file=CLASSES
#mernst thanks for your kind response.
I'm following the heroku tutorial for Heroku/Facebook integration (but I suspect this issue has nothing to do with facebook integration) and I got stuck on the stage where I was supposed to start foreman (I've installed the Heroku installbelt for windows, which includes foreman):
> foreman start
gives:
C:/RailsInstaller/Ruby1.8.7/lib/ruby/site_ruby/1.8/rubygems/dependency.rb:247:in `to_specs': Could not find foreman (>= 0) amongst [POpen4-0.1.4, Platform-0.4.0, ZenTest-4.6.2, abstract-1.0.0, actionm
ailer-3.0.11, actionmailer-3.0.9, actionpack-3.0.11, actionpack-3.0.9, activemodel-3.0.11, activemodel-3.0.9, activerecord-3.0.11, activerecord-3.0.9, activerecord-sqlserver-adapter-3.0.15, activereso
urce-3.0.11, activeresource-3.0.9, activesupport-3.0.11, activesupport-3.0.9, addressable-2.2.6, annotate-2.4.0, arel-2.0.10, autotest-4.4.6, autotest-growl-0.2.16, autotest-rails-pure-4.1.2, autotest
-standalone-4.5.8, builder-2.1.2, bundler-1.0.15, diff-lcs-1.1.3, erubis-2.6.6, factory_girl-1.3.3, factory_girl_rails-1.0, faker-0.3.1, gravatar_image_tag-1.0.0.pre2, heroku-2.14.0, i18n-0.5.0, json-
1.6.1, launchy-2.0.5, mail-2.2.19, mime-types-1.17.2, mime-types-1.16, nokogiri-1.5.0-x86-mingw32, open4-1.1.0, pg-0.11.0-x86-mingw32, polyglot-0.3.3, polyglot-0.3.1, rack-1.2.4, rack-1.2.3, rack-moun
t-0.6.14, rack-test-0.5.7, rails-3.0.11, rails-3.0.9, railties-3.0.11, railties-3.0.9, rake-0.9.2.2, rake-0.8.7, rb-readline-0.4.0, rdoc-3.11, rdoc-3.8, rest-client-1.6.7, rspec-2.6.0, rspec-core-2.6.
4, rspec-expectations-2.6.0, rspec-mocks-2.6.0, rspec-rails-2.6.1, rubygems-update-1.8.11, rubyzip-0.9.4, rubyzip2-2.0.1, spork-0.9.0.rc8-x86-mingw32, sqlite3-1.3.3-x86-mingw32, sqlite3-ruby-1.3.3, te
rm-ansicolor-1.0.7, thor-0.14.6, tiny_tds-0.4.5-x86-mingw32, treetop-1.4.10, treetop-1.4.9, tzinfo-0.3.31, tzinfo-0.3.29, webrat-0.7.1, will_paginate-3.0.pre2, win32-api-1.4.8-x86-mingw32, win32-open3
-0.3.2-x86-mingw32, win32-process-0.6.5, windows-api-0.4.0, windows-pr-1.2.1, zip-2.0.2] (Gem::LoadError)
from C:/RailsInstaller/Ruby1.8.7/lib/ruby/site_ruby/1.8/rubygems/dependency.rb:256:in `to_spec'
from C:/RailsInstaller/Ruby1.8.7/lib/ruby/site_ruby/1.8/rubygems.rb:1210:in `gem'
from C:/Program Files (x86)/ruby-1.9.3/bin/foreman:18
Since I'm a complete noob in this I'm not sure if my question here is a duplicate for Error on 'foreman start' while following the Python/Flask Heroku tutorial (because it's not quite the same error). If so, does anyone have a method for deploying a development environment on windows (for Heruko, Python, Facebook app)? Or should I use Ubuntu for this?
Thanks
Although this question doesn't seem to be of interest to anyone here (5 views in ~2 hours, 0 answers, 0 comments...), I have found the solution and ready to share it with anyone that will encounter it:
Install the latest ruby from rubyinstaller.org (1.9.3-p194) - Sometimes there is a collision installs of the same version, in my case I've just uninstalled all versions of ruby, but if you already have other application that needs older version then you have to be more careful
Check that your system is default to use this version by invoking ruby -v in command line prompt: and getting ruby 1.9.3p194 (2012-04-20) [i386-mingw32] (you may have to close and re-open cmd, to include the new environment variables)
Still in cmd, invoke:
gem install foreman
gem install taps
now go to your Procfile app (e.g. your heroku example app from the tutorial) and execute foreman start, you should see something like this:
18:23:52 web.1 | started with pid 7212
18:23:54 web.1 | * Running on http://0.0.0.0:5000/
18:23:54 web.1 | * Restarting with reloader
after manually adding the ruby path to my system PATH environment variable (Win 7), it still didn't work.
i had to change the default install path of Heroku from
C:\Program Files(x86)\Heroku
to
C:\Heroku
as it didn't properly handle the space in the path. I also tried C:\PROGRA~2\Heroku\ruby-1.9.2\bin to no avail. I imagine any space-less path will do.
hth
I tried
$java -jar ../lib/pmd-5.0.0.jar /var/lib/jenkins/jobs/MYPROJECT/workspace/ xml
error:
Failed to load Main-Class manifest attribute from
../lib/pmd-5.0.0.jar
as per docs from PMD
i also tried:
$java -jar ../lib/pmd-5.0.0.jar /var/lib/jenkins/jobs/MYPROJECT/workspace/ xml java-basic,java-design -encoding UTF-8
Failed to load Main-Class manifest attribute from
../lib/pmd-5.0.0.jar
resolved it by using the following Syntax:
cd ../pmd/bin
./run.sh pmd /var/lib/jenkins/workspace/MYPROJECT/ xml java-basic,java-design -encoding UTF-8 | tee ../../MYPROJECT/pmd.xml
Where do you see that in the doc you linked to?
All of the examples I see on that page say to run java using the PMD class name rather than with the -jar flag. (Which is what I use when running PMD)
Which gives you something like:
java net.sourceforge.pmd.PMD /var/lib/jenkins/jobs/MYPROJECT/workspace/ xml rulesets/java/imports.xml