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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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Shapemapper2 installation issue on oracle linux #40

Open GunjanVasudeva22 opened 1 year ago

GunjanVasudeva22 commented 1 year ago

I am trying to install shapemapper2 on oracle Linux version 8.5, but it finishes with the error every time. But it is working fine for ubuntu. I have only access to oracle Linux. Can you please look into this? Here I am sharing the error details.

Started ShapeMapper v2.1.5 at 2023-01-10 14:40:42 Output will be logged to example-results_shapemapper_log.txt Running from directory: /home/gunjan/Desktop/Biotools/shapemapper-2.1.5 args: --name example-results --target example_data/TPP.fa --amplicon --overwrite --min-depth 1000 --modified --folder example_data/TPPplus --untreated --folder example_data/TPPminus --denatured --folder example_data/TPPdenat Created pipeline at 2023-01-10 14:40:42 Running PrimerLocator at 2023-01-10 14:40:42 . . . . . . done at 2023-01-10 14:40:42 Running FastaFormatChecker at 2023-01-10 14:40:42 . . . . . . done at 2023-01-10 14:40:42 Running BowtieIndexBuilder at 2023-01-10 14:40:42 . . . . . . done at 2023-01-10 14:40:43 Running process group 4 at 2023-01-10 14:40:43 . . . Including these components: Appender1 . . . started at 2023-01-10 14:40:43 Appender2 . . . started at 2023-01-10 14:40:43 ProgressMonitor . . . started at 2023-01-10 14:40:43 QualityTrimmer1 . . . started at 2023-01-10 14:40:43 QualityTrimmer2 . . . started at 2023-01-10 14:40:43 Interleaver . . . started at 2023-01-10 14:40:43 Merger . . . started at 2023-01-10 14:40:43 Tab6Interleaver . . . started at 2023-01-10 14:40:43 BowtieAligner . . . started at 2023-01-10 14:40:43 MutationParser_Modified . . . started at 2023-01-10 14:40:43 MutationCounter_Modified . . . started at 2023-01-10 14:40:43

ERROR: Component "Tab6Interleaver" (sample:Modified) failed, giving the following error message: Traceback (most recent call last): File "/home/gunjan/Desktop/Biotools/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/tab6_interleave.py", line 70, in o.write('\t'.join(fields) + '\n') BrokenPipeError: [Errno 32] Broken pipe

I have tried to check the tab6_interleave.py, it shows FIXE ME IN C++

!/usr/bin/env python3

import sys, os from argparse import ArgumentParser

ap = ArgumentParser() ap.add_argument("--input", type=str) ap.add_argument("--R1", type=str) ap.add_argument("--R2", type=str) ap.add_argument('--output', type=str)

FIXME: rewrite in c++

def iterate_fastq(filename): f = open(filename, "rU") lines = [] for line in f:

suppress jdb socket message

    if line.startswith("Listening"):
        continue
    lines.append(line)
    if len(lines) == 4:
        l = [lines[0][1:].split()[0], lines[1].strip(), lines[3].strip()]
        yield l
        lines = []

pa = ap.parse_args()

Could you please fix this issue? Thanks

cjgunnar commented 1 year ago

See this issue comment: https://github.com/Weeks-UNC/shapemapper2/issues/12#issuecomment-597352511

Our group solved the problem on CentOS 8 Linux by installing libnsl library via the package manager

dnf install libnsl

From what I can tell Oracle also uses dnf so the same solution might work.