define alternative rules with snakemake
Hello I am new with snakemake and I need some help.
My goal is to index a genome (with bowtie2)
But I need some alternative steps depending of the files that are available
1> check if index already exist in storage (/storage/index)
2> if yes, copy index in local (/index)
3> if no, create index in local (/index)
4> then copy new index in storage (/storage/index)
I managed to setup a bash script to check the existing file and the alternative workflows. But I wish to use snakemake and I am not sure how to define the rules to obtain a similar behavior.
snakemake
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
add a comment |
Hello I am new with snakemake and I need some help.
My goal is to index a genome (with bowtie2)
But I need some alternative steps depending of the files that are available
1> check if index already exist in storage (/storage/index)
2> if yes, copy index in local (/index)
3> if no, create index in local (/index)
4> then copy new index in storage (/storage/index)
I managed to setup a bash script to check the existing file and the alternative workflows. But I wish to use snakemake and I am not sure how to define the rules to obtain a similar behavior.
snakemake
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53
add a comment |
Hello I am new with snakemake and I need some help.
My goal is to index a genome (with bowtie2)
But I need some alternative steps depending of the files that are available
1> check if index already exist in storage (/storage/index)
2> if yes, copy index in local (/index)
3> if no, create index in local (/index)
4> then copy new index in storage (/storage/index)
I managed to setup a bash script to check the existing file and the alternative workflows. But I wish to use snakemake and I am not sure how to define the rules to obtain a similar behavior.
snakemake
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
Hello I am new with snakemake and I need some help.
My goal is to index a genome (with bowtie2)
But I need some alternative steps depending of the files that are available
1> check if index already exist in storage (/storage/index)
2> if yes, copy index in local (/index)
3> if no, create index in local (/index)
4> then copy new index in storage (/storage/index)
I managed to setup a bash script to check the existing file and the alternative workflows. But I wish to use snakemake and I am not sure how to define the rules to obtain a similar behavior.
snakemake
snakemake
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
asked Jan 2 at 7:47
Maxime HebrardMaxime Hebrard
285
285
I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53
add a comment |
I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53
I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53
I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53
add a comment |
1 Answer
1
active
oldest
votes
Your psedocode logic, as it is, seems to create cyclical dependency problem in snakemake. So to make it simpler, I changed step3 to if no, create new index in storage (/storage/index) and this allows step4 to be same as step1.
rule create_index:
input:
"/storage/index/a.fa"
output:
"/storage/index/a.idx"
message:
"Create index at source dir"
shell:
'''
index_tool {input} {output}
'''
rule copy_index:
input:
"/storage/index/a.idx"
output:
"/local/index/a.idx"
message:
"copy index to local dir"
shell:
'''
cp {input} {output}
'''
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you excludeinput:, just defineoutput:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.
– JeeYem
Jan 3 at 15:59
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
Your psedocode logic, as it is, seems to create cyclical dependency problem in snakemake. So to make it simpler, I changed step3 to if no, create new index in storage (/storage/index) and this allows step4 to be same as step1.
rule create_index:
input:
"/storage/index/a.fa"
output:
"/storage/index/a.idx"
message:
"Create index at source dir"
shell:
'''
index_tool {input} {output}
'''
rule copy_index:
input:
"/storage/index/a.idx"
output:
"/local/index/a.idx"
message:
"copy index to local dir"
shell:
'''
cp {input} {output}
'''
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you excludeinput:, just defineoutput:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.
– JeeYem
Jan 3 at 15:59
add a comment |
Your psedocode logic, as it is, seems to create cyclical dependency problem in snakemake. So to make it simpler, I changed step3 to if no, create new index in storage (/storage/index) and this allows step4 to be same as step1.
rule create_index:
input:
"/storage/index/a.fa"
output:
"/storage/index/a.idx"
message:
"Create index at source dir"
shell:
'''
index_tool {input} {output}
'''
rule copy_index:
input:
"/storage/index/a.idx"
output:
"/local/index/a.idx"
message:
"copy index to local dir"
shell:
'''
cp {input} {output}
'''
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you excludeinput:, just defineoutput:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.
– JeeYem
Jan 3 at 15:59
add a comment |
Your psedocode logic, as it is, seems to create cyclical dependency problem in snakemake. So to make it simpler, I changed step3 to if no, create new index in storage (/storage/index) and this allows step4 to be same as step1.
rule create_index:
input:
"/storage/index/a.fa"
output:
"/storage/index/a.idx"
message:
"Create index at source dir"
shell:
'''
index_tool {input} {output}
'''
rule copy_index:
input:
"/storage/index/a.idx"
output:
"/local/index/a.idx"
message:
"copy index to local dir"
shell:
'''
cp {input} {output}
'''
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
Your psedocode logic, as it is, seems to create cyclical dependency problem in snakemake. So to make it simpler, I changed step3 to if no, create new index in storage (/storage/index) and this allows step4 to be same as step1.
rule create_index:
input:
"/storage/index/a.fa"
output:
"/storage/index/a.idx"
message:
"Create index at source dir"
shell:
'''
index_tool {input} {output}
'''
rule copy_index:
input:
"/storage/index/a.idx"
output:
"/local/index/a.idx"
message:
"copy index to local dir"
shell:
'''
cp {input} {output}
'''
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
answered Jan 2 at 23:21
JeeYemJeeYem
1,227924
1,227924
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you excludeinput:, just defineoutput:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.
– JeeYem
Jan 3 at 15:59
add a comment |
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you excludeinput:, just defineoutput:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.
– JeeYem
Jan 3 at 15:59
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I get your point. But in my setup I cannot create the index directly in storage. I need to create the index in local then copy into storage.
– Maxime Hebrard
Jan 3 at 9:45
I assumed this would be possible because of your step4. An ugly workaround is you exclude
input:, just define output:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.– JeeYem
Jan 3 at 15:59
I assumed this would be possible because of your step4. An ugly workaround is you exclude
input:, just define output:, and let your bash script do the job for you. Of course, you will be missing out on snakemake's advantages.– JeeYem
Jan 3 at 15:59
add a comment |
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I would suggest showing what you have tried so far and where you ran into problems.
– JeeYem
Jan 2 at 16:53