Error in Clustal W and repAlignLineage

[huangyan530]

❓ Questions and Help

Hello, I'm a new user of immunarch and I've question about the Clustal W. Fisrtly, I have already installed Clustal W according to the guide: https://www.howtoinstall.me/ubuntu/18-04/clustalw/. Then, run the app of ClustalW2.exe. Finally, I input the following code in Rstudio, but error happened. What can I do for solve this issue, thank you very much.

---

Code(example code, without changing) data(bcrdata)

bcr_data <- bcrdata$data %>% top(500) bcr_data %>%

• seqCluster(seqDist(bcr_data), .fixed_threshold = 3) %>%
• repGermline(.threads = 1) %>%
• repAlignLineage(.min_lineage_sequences = 2) Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed!\n", : repAlignLineage requires Clustal W app to be installed! Please download it from here: http://www.clustal.org/download/current/ or install it with your system package manager (such as apt or dnf). ——————————————————————————————————————————

By the way，I have another question，I found that it instead of accumulating counts of the same clonotype, the V and U gene usage analyses seemed to count only those corresponding to clonotype. Is that true? How can I figure it? Thank you, I am looking forward to your reply. Dr. Huang

[Alexander230]

Hello, Dr. Huang!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

About your 1st question: on some systems, Clustal executable is named clustal2 instead of clustal. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="bcr-pipeline-fixes")
devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

[huangyan530]

Hello， Professor Aleksandr Popov

Thank you reply to me so quickly.

I have tried to install immunarch from a branch with this fix using the following commands. However, the previous problem remains——"Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed! \ n ". Besides, the software which I use is clustal w2.1. Thank you for helping me to solve this problem! I am looking forward to your reply! Sincerely， Dr Huang

At 2022-10-12 21:34:29, "Aleksandr Popov" @.***> wrote:

Hello, Dr. Huang!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

About your 1st question: on some systems, Clustal executable is named clustal2 instead of clustal. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="bcr-pipeline-fixes") devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[Alexander230]

Please check your PATH variable, whether it includes the path to clustalw or clustalw2 executable. You can check it with which clustalw and which clustalw2 commands on Linux or Mac, and with where clustalw2 on Windows (in system console, not in R console). If these commands don't return a correct path to the program, probably you need to add the path manually. You can search online how to edit the PATH variable in your operating system or distro.

Cheers, Aleksandr

[huangyan530]

Hello， Professor Aleksandr Popov

I have tried to install immunarch from a branch with this fix using the following commands. However, the previous problem remains——"Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed! \ n ". Besides, the software which I use is clustal w2.1. How can I solve this problem？ I am looking forward to your reply! Sincerely， Dr Huang

At 2022-10-12 21:34:29, "Aleksandr Popov" @.***> wrote:

Hello, Dr. Huang!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

About your 1st question: on some systems, Clustal executable is named clustal2 instead of clustal. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="bcr-pipeline-fixes") devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[huangyan530]

Hello， Professor Aleksandr Popov

I have tried to install immunarch from a branch with this fix using the following commands. However, the previous problem remains——"Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed! \ n ". Besides, the software which I use is clustal w2.1. How can I solve this problem？ I am looking forward to your reply! Sincerely， Dr Huang

At 2022-10-12 21:34:29, "Aleksandr Popov" @.***> wrote:

Hello, Dr. Huang!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

About your 1st question: on some systems, Clustal executable is named clustal2 instead of clustal. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="bcr-pipeline-fixes") devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[huangyan530]

Hello Professor Aleksandr Popov, Thank you for your reply before. I have add the new path variable to system, but the R studio remain can not be operated. Thank you very much, I am looking forward to your reply! urgently！！

At 2022-10-17 21:12:03, "黄燕" @.***> wrote:

Hello， Professor Aleksandr Popov

I have tried to install immunarch from a branch with this fix using the following commands. However, the previous problem remains——"Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed! \ n ". Besides, the software which I use is clustal w2.1. How can I solve this problem？ I am looking forward to your reply! Sincerely， Dr Huang

At 2022-10-12 21:34:29, "Aleksandr Popov" @.***> wrote:

Hello, Dr. Huang!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

About your 1st question: on some systems, Clustal executable is named clustal2 instead of clustal. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="bcr-pipeline-fixes") devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[Alexander230]

Hi, Huang!

If you created a new variable, it's probably a wrong place, because every system must have the existing PATH variable. Here are the instructions how to change it on Windows https://www.wikihow.com/Change-the-PATH-Environment-Variable-on-Windows, Mac OS https://stackoverflow.com/questions/7703041/editing-path-variable-on-mac and Linux https://superuser.com/questions/488173/how-can-i-edit-the-path-on-linux . After this, reboot and check if your path to Clustal is now included in your PATH (echo $PATH on Linux/Mac, echo %PATH% on Windows). Also try to launch clustalw / clustalw2 from command line to check that OS can find it.

If it works, run R and execute Sys.getenv("PATH") command to check that the path visible from R, and then Sys.which("clustalw") and Sys.which("clustalw2") to check that at least one of these 2 commands returns not empty path.

Cheers, Aleksandr

[huangyan530]

Hello，Aleksandr！ Thank you for your early reply！ I have already changed the PATH on Windows11（Figure1）. Now，I am sure that the path to Clustal is included in my PATH（Figure2）. However, the previous problem remains——"Error in require_system_package("clustalw", error_message = paste0("repAlignLineage requires Clustal W app to be installed! \ n ". I have no idea to figure out it. Thank you for helping me for a long time. I hope you happy everyday, sincerely. Dr Huang.

Figure1

Figure2

Figure3

At 2022-10-18 22:26:55, "Aleksandr Popov" @.***> wrote:

Hi, Huang!

If you created a new variable, it's probably a wrong place, because every system must have the existing PATH variable. Here are the instructions how to change it on Windows https://www.wikihow.com/Change-the-PATH-Environment-Variable-on-Windows, Mac OS https://stackoverflow.com/questions/7703041/editing-path-variable-on-mac and Linux https://superuser.com/questions/488173/how-can-i-edit-the-path-on-linux . After this, reboot and check if your path to Clustal is now included in your PATH (echo $PATH on Linux/Mac, echo %PATH% on Windows). Also try to launch clustalw / clustalw2 from command line to check that OS can find it.

If it works, run R and execute Sys.getenv("PATH") command to check that the path visible from R, and then Sys.which("clustalw") and Sys.which("clustalw2") to check that at least one of these 2 commands returns not empty path.

Cheers, Aleksandr

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[ncborcherding]

Hey @huangyan530

I was running into a similar issue on mac. I had clustalw installed and could run it via command line.

I ended up reinstalling clustalw using conda, then pointing RStudio to my conda:

Command Line:

 conda install -c bioconda clustalw

Rstudio:

Sys.setenv(PATH=paste0('/Users/ncborch/opt/anaconda3/bin:', Sys.getenv('PATH')))
#Will need to change the path of this to your conda instance

It was only then I got:

Sys.which("clustalw2")

clustalw2 "/Users/ncborch/opt/anaconda3/bin/clustalw2"

[Alexander230]

Hi, @huangyan530 and @ncborcherding!

I've made a tutorial how to install Clustal and Phylip on Windows and add paths to executables, so R can find them: Clustal.and.Phylip.installation.tutorial.zip

On macOS there is /etc/paths file, where you can manually add paths to installed and unzipped executables; here is the instruction: https://www.architectryan.com/2012/10/02/add-to-the-path-on-mac-os-x-mountain-lion/

After editing /etc/paths, I think you also need to restart Rstudio to make Sys.which() command find executables on these paths.

Best regards, Aleksandr