Comments (9)
ebergstr
commented on June 17, 2024
1
Downloading from the Sanger FTP site will not work for directly transferring into the site-packages. You can download the final reference files from ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/[desired_genome].tar.gz using wget or rsync
and then transfer that file into your C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/ directory. You will then need to unzip the file (see below for all steps):
wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz
move GRCh37.tar.gz C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/
tar -xzf C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz -C C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/
Hope this helps!
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vellamike
commented on June 17, 2024
What does the full traceback say
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XuanYuXu
commented on June 17, 2024
What does the full traceback say
It says I do not have the tar.gz file,if that file only exits in linux system?because I use windows system
In [4]: %tb
FileNotFoundError Traceback (most recent call last)
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp)
436 os.system("tar -xzf " + ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz -C " + ref_dir + "/references/chromosomes/tsb/")
--> 437 os.remove(ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz")
438 except:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。: 'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
During handling of the above exception, another exception occurred:
SystemExit Traceback (most recent call last)
in
----> 1 genInstall.install('GRCh37')
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp)
438 except:
439 print("The ensembl ftp site is not currently responding.")
--> 440 sys.exit()
441 else:
442 print("Direct download for RSYNC is not yet supported")
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vellamike
commented on June 17, 2024
I'm not sure about windows. The error is saying that ENSEMBL FTP is down,
but it seems to be fine. Can you download the file manually and place it in
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
?
…On Wed, Mar 4, 2020 at 12:44 PM XuanYuXu ***@***.***> wrote:
What does the full traceback say
It says I do not have the tar.gz file,if that file only exits in linux
system?because I use windows system
In [4]: %tb
------------------------------
FileNotFoundError Traceback (most recent call last)
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp)
436 os.system("tar -xzf " + ref_dir + "/references/chromosomes/tsb/" +
genome + ".tar.gz -C " + ref_dir + "/references/chromosomes/tsb/")
--> 437 os.remove(ref_dir + "/references/chromosomes/tsb/" + genome +
".tar.gz")
438 except:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。:
'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
During handling of the above exception, another exception occurred:
SystemExit Traceback (most recent call last)
in
----> 1 genInstall.install('GRCh37')
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp)
438 except:
439 print("The ensembl ftp site is not currently responding.")
--> 440 sys.exit()
441 else:
442 print("Direct download for RSYNC is not yet supported")
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XuanYuXu
commented on June 17, 2024
I'm not sure about windows. The error is saying that ENSEMBL FTP is down, but it seems to be fine. Can you download the file manually and place it in C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz' ?
…
On Wed, Mar 4, 2020 at 12:44 PM XuanYuXu @.***> wrote: What does the full traceback say It says I do not have the tar.gz file,if that file only exits in linux system?because I use windows system In [4]: %tb ------------------------------ FileNotFoundError Traceback (most recent call last) C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp) 436 os.system("tar -xzf " + ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz -C " + ref_dir + "/references/chromosomes/tsb/") --> 437 os.remove(ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz") 438 except: FileNotFoundError: [WinError 2] 系统找不到指定的文件。: 'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz' During handling of the above exception, another exception occurred: SystemExit Traceback (most recent call last) in ----> 1 genInstall.install('GRCh37') C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp) 438 except: 439 print("The ensembl ftp site is not currently responding.") --> 440 sys.exit() 441 else: 442 print("Direct download for RSYNC is not yet supported") — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#16?email_source=notifications&email_token=AALYB7J62IM4AHKW2NV6LBDRFZEJ5A5CNFSM4LBFAWYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENXVJVI#issuecomment-594498773>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALYB7OR7YONFCAJKZAOMT3RFZEJ5ANCNFSM4LBFAWYA .
I'm not sure about windows. The error is saying that ENSEMBL FTP is down, but it seems to be fine. Can you download the file manually and place it in C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz' ?
…
On Wed, Mar 4, 2020 at 12:44 PM XuanYuXu @.***> wrote: What does the full traceback say It says I do not have the tar.gz file,if that file only exits in linux system?because I use windows system In [4]: %tb ------------------------------ FileNotFoundError Traceback (most recent call last) C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp) 436 os.system("tar -xzf " + ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz -C " + ref_dir + "/references/chromosomes/tsb/") --> 437 os.remove(ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz") 438 except: FileNotFoundError: [WinError 2] 系统找不到指定的文件。: 'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz' During handling of the above exception, another exception occurred: SystemExit Traceback (most recent call last) in ----> 1 genInstall.install('GRCh37') C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in install(genome, custom, rsync, bash, ftp) 438 except: 439 print("The ensembl ftp site is not currently responding.") --> 440 sys.exit() 441 else: 442 print("Direct download for RSYNC is not yet supported") — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#16?email_source=notifications&email_token=AALYB7J62IM4AHKW2NV6LBDRFZEJ5A5CNFSM4LBFAWYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENXVJVI#issuecomment-594498773>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALYB7OR7YONFCAJKZAOMT3RFZEJ5ANCNFSM4LBFAWYA .
But I do not know where I can dowload that file,did you have that file when you install this package?
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vellamike
commented on June 17, 2024
Should be available here ftp://ftp.ensembl.org/pub/ (not sure exactly where)
…On Wed, Mar 4, 2020 at 12:54 PM XuanYuXu ***@***.***> wrote:
I'm not sure about windows. The error is saying that ENSEMBL FTP is down,
but it seems to be fine. Can you download the file manually and place it in
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
?
… <#m_-4382863112387544121_>
On Wed, Mar 4, 2020 at 12:44 PM XuanYuXu *@*.***> wrote: What does the
full traceback say It says I do not have the tar.gz file,if that file only
exits in linux system?because I use windows system In [4]: %tb
------------------------------ FileNotFoundError Traceback (most recent
call last)
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp) 436 os.system("tar -xzf " +
ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz -C " + ref_dir
+ "/references/chromosomes/tsb/") --> 437 os.remove(ref_dir +
"/references/chromosomes/tsb/" + genome + ".tar.gz") 438 except:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。:
'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
During handling of the above exception, another exception occurred:
SystemExit Traceback (most recent call last) in ----> 1
genInstall.install('GRCh37')
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp) 438 except: 439 print("The
ensembl ftp site is not currently responding.") --> 440 sys.exit() 441
else: 442 print("Direct download for RSYNC is not yet supported") — You are
receiving this because you commented. Reply to this email directly, view it
on GitHub <#16
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or unsubscribe
https://github.com/notifications/unsubscribe-auth/AALYB7OR7YONFCAJKZAOMT3RFZEJ5ANCNFSM4LBFAWYA
.
I'm not sure about windows. The error is saying that ENSEMBL FTP is down,
but it seems to be fine. Can you download the file manually and place it in
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
?
… <#m_-4382863112387544121_>
On Wed, Mar 4, 2020 at 12:44 PM XuanYuXu *@*.***> wrote: What does the
full traceback say It says I do not have the tar.gz file,if that file only
exits in linux system?because I use windows system In [4]: %tb
------------------------------ FileNotFoundError Traceback (most recent
call last)
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp) 436 os.system("tar -xzf " +
ref_dir + "/references/chromosomes/tsb/" + genome + ".tar.gz -C " + ref_dir
+ "/references/chromosomes/tsb/") --> 437 os.remove(ref_dir +
"/references/chromosomes/tsb/" + genome + ".tar.gz") 438 except:
FileNotFoundError: [WinError 2] 系统找不到指定的文件。:
'C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh37.tar.gz'
During handling of the above exception, another exception occurred:
SystemExit Traceback (most recent call last) in ----> 1
genInstall.install('GRCh37')
C:\Anaconda3\lib\site-packages\SigProfilerMatrixGenerator\install.py in
install(genome, custom, rsync, bash, ftp) 438 except: 439 print("The
ensembl ftp site is not currently responding.") --> 440 sys.exit() 441
else: 442 print("Direct download for RSYNC is not yet supported") — You are
receiving this because you commented. Reply to this email directly, view it
on GitHub <#16
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But I do not know where I can dowload that file,did you have that file
when you install this package?
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superjw
commented on June 17, 2024
I just did a test install on Linux, it seems fine with me. Not too sure about windows either. But if you want to download the reference file, I fairly confident you should download from the following link.
ftp://ngs.sanger.ac.uk/scratch/project/mutographs/SigProf/
As far as I know, the reference is compiled someway and it is not the standard reference file from Ensembl.
Give it a go and let us know what happens.
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XuanYuXu
commented on June 17, 2024
OK，thanks a lot ,I try downloading that file ,and hope that works .
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XuanYuXu
commented on June 17, 2024
Thanks a lot ,I try dowloading that file ,and hope it works !
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