Comments (5)
I encountered the same error. I believe this is a problem with the cufflinks
package from Debianโnot the upstream cufflinks. The package maintainers apply a patch to make cuffmerge work with Python 3, but it seems they neglected to change the calls to open
. Here's a short patch that should fix it.
--- a/src/cuffmerge
+++ b/src/cuffmerge
@@ -56,6 +56,21 @@
def __init__(self, msg):
self.msg = msg
+# Unbuffered class from Magnus Lycka
+# Wraps a stream so that writes are always flushed.
+# https://mail.python.org/pipermail/tutor/2003-November/026645.html
+class Unbuffered(object):
+ def __init__(self, stream):
+ self.stream = stream
+ def write(self, data):
+ self.stream.write(data)
+ self.stream.flush()
+ def writelines(self, datas):
+ self.stream.writelines(datas)
+ self.stream.flush()
+ def __getattr__(self, attr):
+ return getattr(self.stream, attr)
+
class TestParams:
class SystemParams:
@@ -523,7 +538,7 @@
start_time = datetime.now()
prepare_output_dir()
- run_log = open(logging_dir + "run.log", "w", 0)
+ run_log = Unbuffered(open(logging_dir + "run.log", "w"))
run_cmd = " ".join(argv)
print(run_cmd, file=run_log)
from cufflinks.
I am also facing the same issue. Could anyone suggest me solution. I am new to this field.
Thanks in advance.
Regards
Rashi
from cufflinks.
I am also facing the same issue. Could anyone suggest me solution. I am new to this field.
Thanks in advance.
Regards Rashi
If you're encountering this issue on Ubuntu 20.04, you can download a version of the cufflinks
package with the patch I suggested applied from my repository here.
The steps are
wget http://cs485repo-archives.s3-website.us-east-2.amazonaws.com/repo/dists/focal/non-free/binary-amd64/science/cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.deb
sudo dpkg -i cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.deb
from cufflinks.
I am also facing the same issue. Could anyone suggest me solution. I am new to this field.
Thanks in advance.
Regards RashiIf you're encountering this issue on Ubuntu 20.04, you can download a version of the
cufflinks
package with the patch I suggested applied from my repository here.The steps are
wget https://www.cs.uky.edu/~acta225/CS485/repo/dists/focal/non-free/binary-amd64/science/cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.deb sudo dpkg -i cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.deb
will this work for Ubuntu 22.04?
from cufflinks.
I am also facing the same issue. Could anyone suggest me solution. I am new to this field.
Thanks in advance.
Regards RashiIf you're encountering this issue on Ubuntu 20.04, you can download a version of the
cufflinks
package with the patch I suggested applied from my repository here.
The steps arewget https://www.cs.uky.edu/~acta225/CS485/repo/dists/focal/non-free/binary-amd64/science/cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.deb sudo dpkg -i cufflinks_2.2.1+dfsg.1-9~ngs+1_amd64.debwill this work for Ubuntu 22.04?
I have a version for 22.04 now here.
wget https://www.cs.uky.edu/~acta225/CS485/repo/dists/jammy/non-free/binary-amd64/science/cufflinks_2.2.1+dfsg.1-10~ngs+1_amd64.deb
sudo dpkg -i cufflinks_2.2.1+dfsg.1-10~ngs+1_amd64.deb
from cufflinks.
Related Issues (20)
- Please use std::fabs instead of just fabs in C++ to avoid conflicts
- The https version of cufflinks website looks broken
- Please add the corresponding ifdef for the code meant only for MinGW
- -m64 breaks build on architectures other than amd64
- configure error: We could not detect the bam libraries
- error: reference to 'thread' is ambiguous HOT 1
- Correlation between replicates
- Nondeterministic segfault on OSX
- 0 ReadHits still live
- Intron not within scaffold warnings HOT 1
- license clarification
- cuffmerge
- Cuffmerge GTF error
- Performance data of cufflinks in computing speed.
- Cufflinks - Inconsistent Results for SAM/BAM File Sorted by Reference Position
- cuffdiff error: number of labels must match number of conditions
- multithreading
- # coverage and -g and -G
- Unusual behavior of cufflinks when a colon is present in the contig names
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from cufflinks.