Xforce Keygen Make Sure You Can Write To Current Directory
Kylee Evancho
The way my bash prompt is currently configured, it shows the whole path to the current directory. This is annoying when I'm deep inside a directory tree, as the prompt becomes so long that every command wraps into the next line. How do I make it show only the last part of the path?
The PROMPT_COMMAND variable, if set, is a command that gets run before displaying the prompt specified in PS1. In your case, PROMPT_COMMAND runs an echo statement with certain ANSI escape sequences that manipulate the titlebar of an Xterm.
Most of the other solutions did not work for me across all of my OSes that share my dot files: AIX, Windoze, and Linux. The bash ports were old versions that didn't support certain constructs and I didn't want to fork another process (i.e. sed, awk, etc.) which is noticeably expensive under cygwin.
But when I try to run this same macro from the server (i.e. I call this macro from a workflow that is saved into our company gallery and is run from that server machine), the Run Command throws errors (generally "1"), which suggest that one or more of the files can't be created or read.
So then I thought that I could specify a distinct network directory that I know the server box has access to. And while this works fine for the Write Source and Read Results sections, I am unable to use a UNC path in my command line argument.
So my question is: how can I set up this macro so that it can either a) always use a relative path that the machine running the workflow actually has write access to, or b) use a defined network path without running into the UNC issue?
That seemed to resolve the issues on my side (and hopefully it's the same for you). I was able to figure out the issue by adding a pause statement to the bat and then not making it silent. Then I got this from the cmd prompt:
By having it write out the bat to a relative path, it's actually using the macro's relative path. So the bat file is called from my macro repository, which I have in the UNC form. Apparently the cmd prompt balks at that and then uses C:\Windows as the working directory. While I'm using the Engine.tempfilepath constant, you could also use Engine.ModuleDirectory constant.
Your syntax works perfectly fine when I run the workflow on my local machine after I've saved it somewhere. But if I paste the same tools into a new workflow and don't save it (i.e. it is using the workflow constants as a temporary file location), I get the same 255 error.
Thanks for the suggestion. The problem is that whenever I reference either of those constants (the TempFilePath or the WorkflowDirectory), I get errors - either a 1 or a 255, both of which seem to suggest that the run command can't locate one or more of the files.
I don't get any of these errors when I run the workflow from my local machine after I've saved it somewhere explicit. But if it's a new unsaved workflow, or a workflow that I save to the gallery, I can't get this run command to execute.
@mix_pix hmm...it looks like the messages show that the bat is always written correct? If that's the case, I would change your formula tool so that instead of writing your results file to a relative path (results.txt) you write it to to the same temp directory (%ENGINE.tempfilepath%results.txt) as the bat itself. I ran the attached just fine on my server. The yxzp didn't include all the nested macros so you'll have to add those back in.
When I go remove the Read Results file (e.g. results.txt), the workflow runs without issue, even though I am writing to and reading from the same %temp% directory as I was using for the Read Results file.
@mix_pix and I were able to debug over a webex. When working with an unsaved workflow or on the server, the .bat was being run from an unexpected directory. There are at least 3 different ways to fix this
Additional info: The code has been written in Python v 2.7.14 where as the pre installed python setup inside Alteryx seems to be v 3.6. So am unable to run the script via the latest. With some help the code was modified for v 3.6 and it works fine fetching the information required via the IDE. But when I try to use this code in Alteryx using a Run Command it fails and throws an error. As this is my first try using the run Command tool am not very sure if my cofigs or the directory settings are correct.
How do I safely delete all files with a specific extension (e.g. .bak) from current directory and all subfolders using one command-line? Simply, I'm afraid to use rm since I used it wrong once and now I need advice.
First run the command shopt -s globstar. You can run that on the command line, and it'll have effect only in that shell window. You can put it in your .bashrc, and then all newly started shells will pick it up. The effect of that command is to make **/ match files in the current directory and its subdirectories recursively (by default, **/ means the same thing as */: only in the immediate subdirectories). Then:
As Eliah Kagan makes clear in extensive comments, you can also make this recursive using find. In that case you can't use an alias, so the commands below assume you have installed trash-cli. I summarise Eliah's comments:
-xtype f selects files and symlinks to files, but not folders. To delete .bak folders too, remove that part, and use -execdir, which avoids cannot trash non-existent errors for .bak files inside .bak directories:
Edit: To clarify, I meant under a particular subdir, not systemwide. And yes, that means all the permutations and combinations of user, group and world writability that would allow that user to write. I know what the question entails semantically, I was hoping for a one- or few-liner to execute to get a list of these files.
There is plenty of room to optimize this but I'll leave that to someone else... Also, I never can remember all the details of find and crossing filesystems and that sort of nonsense. Also, make sure the output of groups is the same as on my test linux system
This is a rough example of how you'd find files writable by a user. This will when run as any user, but if you run it as a non-uid0 user you'll only find things that are in directories that the user running the script has both read and execute permissions to.
To say "I want to see all files that X account can write to" means every file owned by them with u+w, every file owned by any group they belong to that's set g+w, and every file world writable (o+w).
BUSCO is a software package that requires a number of third-party tools.To simplify installation, BUSCO is available as a Conda package and a Docker image with all dependencies pre-installed.It can also be installed manually though in this case care must be taken to ensure all dependencies are installed and configured correctly.
Conda is an open-source package management and environment management system that simplifies the installation and management of software packages and their dependencies across diverse computing environments.
Docker is a tool for packaging and running applications and their dependencies in isolated containers, streamlining the deployment and management of software across diverse environments.Some familiarity with Docker is required to use the BUSCO Docker image. See the Docker userguide for details.
Use mounts (-v) to exchange files between the host filesystem and the container filesystem. In the following example your current working directory ($(pwd)) is mounted as /busco_wd in the container. This allows you to access files in the current directory from within the container and to write files to the current directory from within the container.
The default working directory in the container is /busco_wd. With your non-root uid, attempts to write in the container virtual filesystem will fail if it is not a mount point. You can redefine the working directory using -w to match another mounted folder as current working directory.For example, if your BUSCO input filepath on your file system is /home/name/genome.fna
Be careful not to specify a host folder that does not exist when using -v /hostfolder/:/dockermount. Docker will create it with the root account, which is useless and annoying. It is safer to use the current directory -v $(pwd):/dockermount
For Augustus, the option --augustus_parameters allows advanced users to freely pass parameters. Use it only to fix biologically relevant parameters such as the translation table and mention these when reporting the result. Do not use it for selecting the Augustus species, as there is a dedicated BUSCO parameter (--augustus_species), and do not use it to specify the number of cpus (-c, --cpu).
During development, we recognised an issue with tBLASTn versions 2.4-2.10.0 when using more than one CPU.NCBI issued a fix for the problem in version 2.10.1+. Make sure you have at least version 2.10.1+ installed.
BUSCO is being developed and tested on multiple distributions of Linux (e.g. Arch Linux, CentOS, Ubuntu). We do not support macOS but BUSCO should work on it, although Augustus seems to cause troubles on some BSD-derived systems, including macOS. Consider the Docker container if you work on incompatible environments.
-i or --in defines the input file to analyse which is either a nucleotide fasta file or a protein fasta file, depending on the BUSCO mode. As of v5.1.0 the input argument can now also be a directorycontaining fasta files to run in batch mode.
-l or --lineage_dataset Specify the name of the BUSCO lineage dataset to be used, e.g. hymenoptera_odb10. A full list of available datasets can be viewed by entering busco --list-datasets.You should always select the dataset that is most closely related to the assembly or gene set you are assessing. If you are unsure, you can use the --auto-lineage option to automatically select the most appropriate dataset.BUSCO will automatically download the requested dataset if it is not already present in the download folder. You can optionally provide a path to a local dataset instead of a name, e.g. -l /path/to/my/dataset.
--augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2" Pass additional parameters to Augustus. See Augustus documentation for parameter options. All parameters should be contained within a single string with no white space, with each parameter separated by a comma.
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