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 am currently building openfoam 1912 from source and have some trouble building paraview. I just build Qt and Cmake but as soon as i type ./makeParaview qt-5.9.9 5.6.3i get the following error:
./makeParaView: 64: local: -DWM_DP: bad variable name
./makeParaView: 64: ./makeParaView: -DOPENFOAM: bad variable name
A similar error occurs when i try to make VTK / Adios2. Any idea where i took the wrong turn?
Greetings
Gabbagandalf
The proper solution is related to shell quoting issues
- flag="$(stripCompilerFlags $flag)"
+ flag="$(stripCompilerFlags "$flag")"
but in the meantime you can simply change the shebang to #!/bin/bash - it is more forgiving.
As discussed and resolved in these GitLab ticket-1 and ticket-2:
The issue seems to be Ubuntu related.
Solution:
Prior to execute ./makeParaview, switch to bash:
Change the first line of makeParaView script to #!/bin/bash
sudo dpkg-reconfigure dash
./makeParaView
I downloaded and installed the latest Ma version of Maxima from source forge. When I try to launch it, I get
“Maxima.app” is damaged and can’t be opened. You should move it to the Trash.
This happens with both available versions, the one with VTK and the one without VTK.
How can I get it running?
I have MacOS 10.12.6
and both versions are here:
https://sourceforge.net/projects/maxima/files/Maxima-MacOS/5.40.0-MacOSX/
Others have run into the same problem. I don't use MacOS so I'm not sure what the problem is. Anyway, take a look at this bug report: #3316: Maxima VTK for Mac 5.40 is corrupt. The person who submitted it reported they got it working by following the advice in the comments.
See also thread 39: https://sourceforge.net/p/maxima/support-requests/39/
This is a really important thread to the larger MacOS community.
I have a MacBook Pro running OS X El Capitan, which is locked down a few versions back from the current MacOS Mojave.
I spent an entire night trying to get every wxMaxima from 5.36 to 5.42 running without success - even compiling from sources.
In desperation I found the thread 39 and entered the line:
(setf sb-impl::default-external-format :utf-8)
into a ~home/.sbclrc file (/Users/myName/.sbclrc). It was only then that the GUI and the Maxima engine could connect and a normal session could be established. Maxima, its maintainers and its users are too important a world resource to be stymied by such an esoteric and non-obvious bug.
A user encountering this bug will first go into the preferences menu and start trying to make sure that the file addresses and port numbers are correct, but experimentation can corrupt these and lead to other problems.
In my case following excerpt from https://sourceforge.net/p/maxima/mailman/message/35910588/ helped:
(0) Double-click the icon of "Terminal.app" in the folder "/Applications/Utilities", then the command-line-user-interface window is opened.
(1) Move the current working directory to the location of the disc image with the command "cd". (e.g. "Downloads" folder)
$ cd $HOME/Downloads
(2) You can check the attribute with the command "ls -l#":
(You will be able to find "com.apple.quarantine" which is the name of the attribute.)
$ ls -l# ./*.dmg
-rw-r--r--# 1 name staff 471227521 6 24 23:17 ./Maxima-5.40.0-VTK-macOS.dmg
com.apple.quarantine 62
(3) Remove the attribute "com.apple.quarantine" with the command "xattr -d com.apple.quarantine ./*.dmg":
$ xattr -d com.apple.quarantine ./Maxima-5.40.0-VTK-macOS.dmg
(4) Verify that the attribute "com.apple.quarantine" was removed:
$ ls -l# ./*.dmg
-rw-r--r-- 1 name staff 471227521 6 24 23:17 ./Maxima-5.40.0-VTK-macOS.dmg
(5) Double-click the icon of the disc image file to open.
After that, you should install Maxima.app into your "Applications" folder ("/Applications"). And you should drag the Launchers icon from the disc image to another place of your filesystem. You can install launchers to anywhere you like.
Then you will be able to launch Maxima with Maxima.app or launchers.
I am trying to run ReSharpers command line tool InspectCode.exe. It's running fine doing it's job with the expected output.
However after my earlier attempt to get plugins to work, this time with the new version it is supposed to be supported. There is a switch in the command line interface that allows to specify the extension you want to use.
/extensions (/x) – allows using ReSharper extensions that affect code analysis. To use an extension, specify its ID, which you can find by opening the extension package page in the ReSharper Gallery, and then the Package Statistics page. Multiple values are separated with the semicolon.
But I cannot get it to work properly. I cannot even provoke any reaction to the /x switch at all. No matter how or what I pass, I get no feedback from the executable and the output is identical. I don't even get an error message when passing obvious garbage.
I tried the following commandlines for the exact same result:
inspectcode.exe /o="rcli.xml" /swea /x="ReSharper.StyleCop" "my.sln"
inspectcode.exe /o="rcli.xml" /swea /x=ReSharper.StyleCop "my.sln"
inspectcode.exe /o="rcli.xml" /swea "my.sln"
inspectcode.exe /o="rcli.xml" /swea /x=ABCDEFG "my.sln"
Result
JetBrains Inspect Code 9.1.1
Running in 64-bit mode, .NET runtime 4.0.30319.18444 under Microsoft Windows NT
6.1.7601 Service Pack 1
Enabled solution-wide analysis according to Inspect Code command line Setting.
Analyzing files
[files]
Inspection report was written to rcli.xml
What am I doing wrong? How to get extensions to work?
I already tried the R# forums, but it took them more then 24h to approve my post and so far I'm not sure someone else even read it.
Unfortunately, the support for extensions was dropped in 9.0 due to the refactorings in the "ReSharper platform". I hope that JetBrains will bring it back soon.
See RSRP-436208.
This is a late answer that might help future readers (like myself). Currently inspectcode.exe will automatically look for and use any NuGet packages that are in the same folder as the executable (source).
Example for CleanCode extension:
if you have a R# instance on some machine and install the extension, it will be placed in C:\Users\{user}\AppData\Local\JetBrains\plugins\MO.CleanCode.5.6.15
copy MO.CleanCode.5.6.15.nupkg and paste it next to inspectcode.exe
when running inspectcode with verbosity = VERBOSE, the extension should appear in the Zones list:
$cmd = "..\JetBrains.ReSharper.CommandLineTools.2019.3.4\inspectcode.exe"
$outputFile = "..\Output\$($outputName).xml"
& $cmd -o="$outputFile" $sln --verbosity=VERBOSE
Zones: (52pcs)[CodeInspectionPageImplZone, DaemonEngineZone,
DaemonZone, IAmd64CpuArchitectureHostZone, IAspMvcZone,
IBatchToolEnvironmentZone, IClrImplementationHost Zone,
IClrPsiLanguageZone, ICodeEditingOptionsPageImplZone,
IConsoleEnvironmentZone, ICppProductZone, ICpuArchitectureHostZone,
IDocumentModelZone, IEnvironmentZone, IHostSolutionZone,
IInspectCodeConsoleEnvironmentZone, IInspectCodeEnvironmentZone,
IInspectCodeZone, ILanguageAspZone, ILanguageBuildScriptsZone,
ILanguageCppZone, I LanguageCSharpZone, ILanguageCssZone,
ILanguageHtmlZone, ILanguageIlZone, ILanguageJavaScriptZone,
ILanguageMsBuildZone, ILanguageNAntZone, ILanguageProtobufZone, ILa
nguageRazorZone, ILanguageRegExpZone, ILanguageResxZone,
ILanguageVBZone, ILanguageXamlZone, INetFrameworkHostZone, INuGetZone,
IOperatingSystemHostZone, IProjectMode lZone,
IPsiAssemblyFileLoaderImplZone, IPsiLanguageZone,
IPublicVisibilityZone, IRdFrameworkZone, IRiderModelZone,
ISinceClr2HostZone, ISinceClr4HostZone, ITextContro lsZone,
IToolsOptionsPageImplZone, IWebPsiLanguageZone, IWindowsNtHostZone,
PsiFeaturesImplZone, ReplaceableByIntelliJPlatformZone, SweaZone]
Packages: (23pcs)[JetBrains.ExternalAnnotations,
JetBrains.Platform.Core.Ide, JetBrains.Platform.Core.IisExpress,
JetBrains.Platform.Core.MsBuild, JetBrains.Platform. Core.Shell,
JetBrains.Platform.Core.Text, JetBrains.Platform.Interop.CommandLine,
JetBrains.Platform.Interop.dotMemoryUnit.Framework,
JetBrains.Platform.Interop.dotMe moryUnit.Interop.Console,
JetBrains.Platform.Interop.dotMemoryUnit.Interop.Ide,
JetBrains.Platform.RdProtocol, JetBrains.Psi.Features.Core,
JetBrains.Psi.Features.Cpp .Src.Core, JetBrains.Psi.Features.src,
JetBrains.Psi.Features.Tasks, JetBrains.Psi.Features.UnitTesting,
JetBrains.Psi.Features.Web.Core, JetBrains.ReSharperAutomatio
nTools.src.CleanupCode,
JetBrains.ReSharperAutomationTools.src.CommandLineCore,
JetBrains.ReSharperAutomationTools.src.CommandLineProducts,
JetBrains.ReSharperAutomat ionTools.src.DuplicatesFinder,
JetBrains.ReSharperAutomationTools.src.InspectCode, MO.CleanCode]
Does anyone know how to extract teletext subtitles?
I have tried ffmpeg, it says
Invalid frame dimensions 0x0
CCExtractor, it says
"Missing ASF header. Abort
telxcc, it says
! Invalid TS packet header; TS seems to be misaligned
I have done a lot of research, but have no luck. Can anyone offer some help!
dvb_subtitles cannot be extracted with ffmpeg easily because is an image that overlays the original. Good explanation: https://stackoverflow.com/a/20887655/2119685
There is a way to extract the dvb_teletext, which normally includes the subtiltes too.
Install the next dependency:
sudo apt-get install libzvbi-dev
Then recompile from source ffmpeg with:
--enable-libzvbi
Good tutorial here on how to compile FFMPEG from source -https://trac.ffmpeg.org/wiki/CompilationGuide/Ubuntu
Then execute the next command to fetch the subtitles to a .srt file:
ffmpeg -txt_format text -i INPUT1 -an -vn -scodec srt test.srt
And voila, your .srt subtitles will be in test.srt
Did you try using gstreamer ? appsrc->tsdemux->fakesink. Make pipeline like this, and then get the PES data from fakesink callback.