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YeoLab / sailor

CWL+Singularity implementation of an RNA editing workflow
BSD 3-Clause "New" or "Revised" License
39 stars 11 forks source link

run sailor with unprivileged installations of singularity #7

Open yywang-hzau opened 3 years ago

yywang-hzau commented 3 years ago

I installed singularity with unprivileged installations, and download executable into an empty directory](https://s3-us-west-1.amazonaws.com/sailor-1.0.4/sailor-1.0.4). and then I marked downloaded programme as executable and tried to run sailor like these './sailor-1.0.4'. however, occurred some errors "ERROR: File "./sailor-1.0.4" is an ext3 format continer image. ERROR: Only SIF and squashfs images can be extracted in unprivileged mode. ERROR: Use singularity build to convert this image to a SIF file using a setuid install of Singularity. FATAL: while extracting ./sailor-1.0.4: not a squashfs root filesystem" I think it is related to the installation of singularity, so I run "singularity build sailor.sif sailor-1.0.4" errors like these"INFO: Starting build... ERROR: while unpacking ext3 image: while attaching image to loop device: permission denied FATAL: While performing build: packer failed to pack: while attaching image to loop device: permission denied" So I want to know whether sailor can be executed without root privilege.

byee4 commented 3 years ago

Sorry, this might be an older image where those options weren't available, but I believe you can convert to sif format if you run it locally (and have root privilages).

yywang-hzau commented 3 years ago

Thank you for your reply, I have solve the problem successfully, and I have got some results. However, I found the reverse.strand result (T-C) cannot be complementary with the forward.strand result (A-G). For example, I caught a site 123456 on chromosome 1 (A-G) in forward.strand but it show 123459 on chromosome 1 (T-C) in reverse.strand. so I wonder to know the relationship between forward result (A-G) and reverse result (T-C).

byee4 commented 3 years ago

Sorry, I don't quite understand the question but the forward and reverse edits are based on the read orientation. So assuming a stranded library, looking at the bam file on the genome browser, you should see A>G edits being called in areas where most of the reads correspond to a negative strand gene.

yywang-hzau commented 3 years ago

Apologize for my confused statement, I just want to know whether  the (T>C) edited sites in the reverse strand represent the complementary for (A>G) but not the (T(U)>C) edit? Best regards Yuanyuan

2021年8月1日 下午4:21，Brian Yee @.***> 写道：

Sorry, I don't quite understand the question but the forward and reverse edits are based on the read orientation. So assuming a stranded library, looking at the bam file on the genome browser, you should see A>G edits being called in areas where most of the reads correspond to a negative strand gene. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

byee4 commented 3 years ago

Hi, yes if the reads are stranded then T>C edits on the opposite strand should look like A>G

LIUXING-bio commented 7 months ago

How to obtain .sif file, Thanks

LIUXING-bio commented 7 months ago

Thank you for your reply, I have solve the problem successfully, and I have got some results. However, I found the reverse.strand result (T-C) cannot be complementary with the forward.strand result (A-G). For example, I caught a site 123456 on chromosome 1 (A-G) in forward.strand but it show 123459 on chromosome 1 (T-C) in reverse.strand. so I wonder to know the relationship between forward result (A-G) and reverse result (T-C).

How to obtain .sif file, Thanks