shapeit command not found - shapeit installation for GWAS phasing - bash

I would like to install the shapeit for GWAS phasing and impuation. I downloaded the Shapeit version for macos from Shapeit website:
https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download
I extracted the file and got the shapeit execuable file, example folder, and licience file.
Next, I open the terminal in Mac, cd the directory to shapeit folder and type the command line as the website guided:
shapeit -B gwas \
-M genetic_map.txt \
-O gwas.phased
And I got the response:
shapeit command not found.
I guess that means i need to install the shapeit or set a path for shapeit. But I don't know how to do. I am very new with Macos.
Could someone help me ?

Try ./shapeit instead of shapeit, or
Run cp shapeit /usr/local/bin first and try again.

Related

wget command using brew in terminal (mac)

wget -E -H -k -K -p -e robots=off -P ./images/ -i./list.txt
./list.txt: No such file or directory
No URLs found in ./list.txt.
Converted links in 0 files in 0 seconds.
I downloaded and installed brew. Further, I installed wget and it's letting me download images one image at a time. However, when I tried the aforementioned command to download images from multiple urls, it's not doing anything. Can someone tell me what I could be doing wrong here?
wget is pretty lucid with description of issue
./list.txt: No such file or directory
apparently there is not file named list.txt inside current dir. Please trying giving full path to list.txt.

How can I resolve a "No such xattr: com.apple.quarantine" error and path error for arduino ide?

I am trying to update my arduino IDE to a newer version so that it will work on IOS Catalina. I am following some instructions on how to make them compatible but I am stuck on this step. I am meant to put this command in:
xattr -d com.apple.quarantine /usr/local/bin/avrdude
But I keep getting this error:
xattr: /usr/local/bin/avrdude: No such xattr: com.apple.quarantine
I am not sure what I did wrong because when I type in this command:
sudo mv avrdude /usr/local/bin
The result I get is:
avrdude and /usr/local/bin/avrdude are identical
which tells me that the file is in the correct position (I think).
My path in the .zshrc is currently set to:
export PATH=/usr/local/bin:/usr/local/avr/bin:$PATH
but when I type in:
printenv PATH
I get something different than the path listed above.
I am sure this is part of the problem, but I am not sure where to begin looking.
When I saw...
No such xattr: com.apple.quarantine
I became root/sudo, and ran it again and it worked without that error.
sudo xattr -d com.apple.quarantine \<filename\>

can't run zipalign.exe in mac [duplicate]

When I try to run Zipalign on an apk I get the error "Command not found"
I am not that familiar with using terminal commands on the MAC but I have navigated to the SDK/Tools folder and run the following command:
zipalign -v 4 Project1.apk Project1-aligned.apk
I get Command not found
I have tried placing the apks in the Tools folder and same result.
Can someone help me to understand where the apks should be located and where I should run zipalign from?
Thanks, I am very frustrated about this as it seems so simple.
You can find correct path with this command:
find ~/Library/Android/sdk/build-tools -name "zipalign"
Perhaps the current directory is not in your path?
Try adding "./" before your command so
./zipalign -v 4 Project1.apk Project1-aligned.apk
You will find the zipalign tool at /path/to/sdk/build-tools/<build-tools-version>/zipalign NOT in the tools folder anymore.
~/Library/Android/sdk/build-tools/xxxx/zipalign
Drag this to terminal or save this in your path.
xxxx -> Version
Zipalign is a command that located at $ANDROID_HOME/build-tools/{android-version}/.
Hope it helped.
A simple one-liner:
This adds a line in your profile, to add the directory which contains the zipalign executable to your path
Then reloads the profile
echo "export PATH=\$PATH:~/Library/Android/sdk/build-tools/23.0.1/" >> ~/.bash_profile && . ~/.bash_profile
Make sure to replace 23.0.1 with your installed version
$ ls -l ~/Library/Android/sdk/build-tools/
total 0
drwxr-xr-x 23.0.1 <---
Now you should be able to use zipalign regardless of your current working dir
$ zipalign
on the mac with the zsh console, my solution was
command 1)
find ~/Library/Android/sdk/build-tools -name "zipalign"
----------------------------------------------------------
/Users/macOs/Library/Android/sdk/build-tools/28.0.3/zipalign
/Users/macOs/Library/Android/sdk/build-tools/26.0.2/zipalign
/Users/macOs/Library/Android/sdk/build-tools/25.0.2/zipalign
/Users/macOs/Library/Android/sdk/build-tools/27.0.3/zipalign
command 2)
echo "export PATH=\$PATH:~/Library/Android/sdk/build-tools/28.0.3/" >> ~/.bash_profile && . ~/.bash_profile
command 3)
ls -l ~/Library/Android/sdk/build-tools/
command 4)
zipalign -v 4 app-release-unsigned.apk nameApp.apk
2hours resume for newbies (like me) :
If you type this command :
zipalign -v 4 platforms/android/app/build/outputs/apk/release/app-release-unsigned.apk app-release.apk
Witch gives you :
command not found: zipalign
It's maybe that the path is somewhere wrong.
If you have this :
Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_201.jdk/Contents/Home/bin/apt" (-1)
It confirms that its not really as it should be. So, to execute zipalign and finally publish your app, you have to go in the correct repository and execute commande.
1. Go to the correct repo to execute command :
The path is cd /Users/xxxyour_user_namexxx/Library/Android/sdk/build-tools/xxxxx/
cd /Users/greg/Library/Android/sdk/build-tools/28.0.3
2. Execute your zipalign command, don't forget to precise the path of apk file :
Obviously, chance "greg" and "myapp" with your user name & app name.
./zipalign -v 4 /Users/greg/Desktop/AppLocal/myapp/platforms/android/app/build/outputs/apk/release/app-release-unsigned.apk /Users/greg/Desktop/AppLocal/myapp/platforms/android/app/build/outputs/apk/release/app-release.apk
Hope it helps.
Search it and reference it... I have it here and reference it like this:
/Users/lioncio/Desktop/adt-bundle-mac-x86_64-20140702/sdk/build-tools/android-4.4W/zipalign bla bla bla (all the options of the command!)
And worked
Relax! , Just Use Locate Command in Terminal WHEREVER it is , it will come out
tom-MacBook-Air:kavform_app tom$ locate zipalign
/Users/tom/Software/android-sdk-macosx/build-tools/24.0.1/zipalign
/Users/tom/Software/android-sdk-macosx/docs/tools/help/zipalign.html
In my case it was burried over here
/Users/tom/Software/android-sdk-macosx/build-tools/24.0.1/zipalign -v 4 /Users/tom/kavwork/kavform/kavform_app/platforms/android/build/outputs/apk/android-release-unsigned.apk BrideToBe.apk
add it to the path
on terminal
find path for zip align
find ~/Library/Android/sdk/build-tools -name "zipalign"
path: /Users/username/Library/Android/sdk/build-tools/26.0.1/zipalign
enter the path found in there
sudo nano /etc/paths
now on new terminal you can see zipalign reco
Solution for Mac
This error basically means that the terminal wasn't able to find the zipalign file.
So you can either type in the full path for your zipalign file with the command (located in your Android build-tools folder)
/Users/username/Library/Android/sdk/build-tools/26.0.1/zipalign -v 4 android-armv7-release-unsigned.apk helloWorld.apk;
If you do not know the location of the zipalign file, then just use this command
find ~/Library/Android/sdk/build-tools -name "zipalign"
If you are working on Windows, change the command prompt to point to the folder containing the zipalign.exe and then run the command. Also, I have found that you are not using the complete command:
zipalign [-f] [-v] 4 Input.apk Output.apk
cd android-sdk/build-tools/22.0.0/ - change directory to android sdk folder, build tools and choose version (I used 22.0.0).
Then at the prompt type:
./zipalign -v 4 /MyApp/android-x86-release-signed.apk ~/MyApp/android-x86-release-signedandzipped.apk
That worked for me. I tried the other solutions above with no success. I just had to run the command withn the proper folder, but that wasn't explained clearly in other resources I checked.
Navigate to the path of the zip align and include that with the command
/Users/ignatiusandrew/Library/Android/sdk/build-tools/25.0.2/zipalign 4 android-release-unsigned.apk igi.apk
Alternatively, if you do not want to add a specific build tools folder to the path, in case it changes in the future, you can use the first result of find command:
$(find ~/Library/Android/sdk/build-tools -name "zipalign" | head -n 1) <your-zipalign-parameters>
It might be especially useful in a CI pipeline.
for me this worked perfectly, I copied the zipalign file from the android path to the folder where I wanted to run command and then typed ./zipalign -v 4 android-release-unsigned.sdk nameofapp.apk
Note: It was on Mac
%ANDROID_HOME%\\build-tools\\25.0.2\\zipalign -v 4 .\\platforms\\android\\build\\outputs\\apk\\input.apk .\\path\\ output.apk
First,
if your android home is set, then you can just
cd $ANDROID_HOME
and
open . (This should be - /Users/username/Library/Android/, you can just cd to that path as well)
Next, navigate to "sdk/build-tools/25.0.3/" (version 25.0.3 in this case, yours may be a different version).
At your terminal (apk prompt), drag zipalign to the terminal and
...../zipalign -v -p 4 my-app-unsigned.apk my-app-unsigned-aligned.apk.
Should work fine.
Hope it helps.
Downloaded zipalign-file from github
zipalign exec copy and paste in your Project1-aligned.apk directory
./zipalign -v 4 Project1.apk Project1-aligned.apk
In my case
I follow below answer
Change directory
/path/to/sdk/build-tools//zipalign
Type
./zipalign instead zipalign
In short ./zipalign is solution for me.
Solution for Jenkins
For Jenkins users using MacOS to build and sign mobile apps who are experiencing this error, the solution could be this:
At the stage where the signature is made:
withEnv(['PATH=/Users/jenkins/Library/Android/sdk/build-tools/29.0.3',
'ANDROID_SDK_ROOT=/Users/jenkins/Library/Android/sdk',
'JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_301.jdk/Contents/Home'])
I am using Windows with git bash/command promt
zipalign.exe needed to be configured in environment variables.
so include sdk folder 'build-tool' with android version folder you are using to build.
e.g. E:\android-sdk\build-tools\22.0.1
it should contain 'zipalign.exe'. now you can user
zipalign -v 4 Project1.apk Project1-aligned.apk
from any location using command line tools.
thumb up for me so i can help more developers.

How I can launch Sublime Text 2 from the Mac OS X Terminal?

I have tried to launch Sublime Text 2 from Terminal, and I have followed the instruction on Github from this link https://gist.github.com/artero/1236170#installation ,but Im steel have problem. Im trying to make ~bin/ directory in Terminal $ mkdir -p /usr/local/bin ,but I`m getting this error : mkdir: /usr/local/bin: Permission denied. How can I fix this.
You need to use the sudo command, which essentially means you are running the command as user root. Be very careful when using sudo, as you can really mess up your system if you type something incorrectly.
To use it, make sure you have Administrator privileges. Then, run
sudo mkdir /usr/local/bin
to make /usr/local/bin, if it doesn't exist already. Then, run
sudo ln -s /Applications/Sublime\ Text\ 2.app/Contents/SharedSupport/bin/subl /usr/local/bin/sublime
to create a sublime symlink in /usr/local/bin. Finally, edit your ~/.profile file to add /usr/local/bin to your PATH, save it, restart Terminal, and you should be all set.
try
sudo mkdir -p /usr/local/bin

sudo: ./install.sh: command not found is not working on Lion

I've been following this tutorial in order to get SimpleOpenNI installed on my mac but I keep getting stuck at installing the OpenNI and NITE components because it requires me to navigate to the folders in Terminal and then run "sudo ./install.sh". I do this and I get this error:
sudo: ./install.sh: command not found
I've installed Command Line Tools in Xcode and everything.
Thanks
The reason why that happens is because the script you are trying to execute needs the right permissions.
Type:
sudo chmod a+x install.sh
and then try again.
In directory of install.sh
prompt$ sh install.sh
first open Terminal, type cd and than drag the map into Terminal and press enter. Now type sudo ./install.sh and it will work. Took me very long to find out. Hope it helps.
.sh scripts should have "\n" line breaks.
"Command not found" also occurs if "\r\n" line breaks are used.
Well at least this is the case on FreeBSD.
You need to run VBoxLinuxAdditions.run as root, not autorun.sh
Once you've inserted the Guest Additions ISO, open Files and open the disc from the sidebar. Then, right-click in the background of the window where autorun.sh is and select
Open in > Terminal
Now you can run the following command to install the Guest Additions:
sudo ./VboxLinuxAdditions.run
I'm a newbie but here is an answer that may help with the sh problem...I am running Armbian on an orange pi prime H5 SBC and I had downloaded and unzipped arduino ide well after 2 hours of searching and trying I hit it ....open the directory where the file you want to open or install is ...now at the top of the directory open a terminal(under file it will say open a terminal here).now the sh filename.sh will work.

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