From a4574c04cfc90f29787c18cac30c736ba723f03e Mon Sep 17 00:00:00 2001 From: Joseph Tran Date: Fri, 10 Apr 2020 23:10:09 +0200 Subject: [PATCH 1/6] fix typo --- requirements.txt | 8 ++++++++ requirments.txt | 3 --- 2 files changed, 8 insertions(+), 3 deletions(-) create mode 100644 requirements.txt delete mode 100644 requirments.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..e82c566 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,8 @@ +# Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4. Scikit-learn now requires Python 3.5 or newer. +#scikit-learn >= 0.18 +scikit-learn > 0.18, < 0.21 +# last numpy release tosupport Python 2.7: see https://docs.scipy.org/doc/numpy/release.html#numpy-1-16-0-release-notes +Numpy <=1.16.0 +# The last SciPy version to do so is SciPy 1.2.x: https://www.scipy.org/scipylib/faq.html#do-numpy-and-scipytill-support-python-2-7 +scipy <=1.2 +tqdm diff --git a/requirments.txt b/requirments.txt deleted file mode 100644 index 193c663..0000000 --- a/requirments.txt +++ /dev/null @@ -1,3 +0,0 @@ -scikit-learn >= 0.18 -Numpy -tqdm From cc5469adc74605ae6fbb811d6ad27c5846e31229 Mon Sep 17 00:00:00 2001 From: Joseph Tran Date: Fri, 10 Apr 2020 23:12:26 +0200 Subject: [PATCH 2/6] fix LINE compile command and python 2.7 requirements versions --- setup.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index 7c03e50..f447169 100644 --- a/setup.py +++ b/setup.py @@ -7,10 +7,12 @@ VERSION = '0.1.0' +INCPATH="/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/sci_env/include" +LIBPATH="/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/sci_env/lib" +LIBS="-lgsl -lgslcblas -lpthread -L{}".format(LIBPATH) def compile_line(): - compile_command = ("g++ LINE/line.cpp -o LINE/line" - "-lgsl -lgslcblas -lpthread") + compile_command = ("g++ -I{} LINE/line.cpp -o LINE/line {}".format(INCPATH, LIBS)) return_code = call(compile_command.split()) if return_code != 0: sys.exit(("LINE compilation has failed." @@ -18,6 +20,10 @@ def compile_line(): compile_line() +## Important notes to requirements: +# 1. Last numpy release tosupport Python 2.7: see https://docs.scipy.org/doc/numpy/release.html#numpy-1-16-0-release-notes +# 2. The last SciPy version to do so is SciPy 1.2.x: https://www.scipy.org/scipylib/faq.html#do-numpy-and-scipytill-support-python-2-7 +# 3. Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4. Scikit-learn now requires Python 3.5 or newer. setup( name="sci", @@ -26,8 +32,9 @@ def compile_line(): author_email='haitham.ashoor@jax.org', packages=find_packages(), install_requires=[ - 'numpy', - 'scikit-learn', + 'numpy<=1.16.0', + 'scipy<=1.2', + 'scikit-learn>=0.19,<=0.20', 'tqdm' ], From 9c4212f8461163475f91a1b7cbaf809dd60bc0fd Mon Sep 17 00:00:00 2001 From: Joseph Tran Date: Fri, 10 Apr 2020 23:12:54 +0200 Subject: [PATCH 3/6] succeed to compile LINE --- LINE/line | Bin 25038 -> 31784 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/LINE/line b/LINE/line index d11d16fb1f018ac26b1dbf54c5b868f12e9422dc..4aaeed8fcddcd714ad96db07c944fee962860781 100755 GIT binary patch literal 31784 zcmeHw3wTu3x%Qq68v>XM2nt^6h#(gs7j6QACcxlei9|>c5u8kBCKsDz(wPaOEiD?b zOs8pSdsO}&+tNFKZ_-n1skIo88mzV_Ra>djp45YOVyLD_m0Ill@4GI0_8u~|eV+68 z`Tyr(!R&8+m-T($`qpKyz4p%DAN8(Uk>_$5I=PK&4PxzMC8a_!ro~hSpu$*SjK*=Y zafLA)_%K0}{0a%cm8mJu3G)@*4ajnP6+atZqU1Ex9ul%#uC%2{ax^rGCC+jtvkK3K z^QTBT4K?4gS0VXU#T33^l%#8DFUQ#IsgnFXo1E}41Aw$eIE9Szi{W6oZdI;ZmDA9p z;-#UECu73jVa3me9`Kkv;+TnH^(*lZ%jK_-jBNP4lGjkj{w9>8pZ{pmVPB){<%&z4 z@?S&7pQ*H^xqklK(w5MymgcsOEwi>Pm_KX&+>%(NWVWa`^;7ox8*3?U=s0==W*BVV znJPa)K@AF!8Lf~j6lA}<9KTByJ_+zj{5<$whTlc_jl++r5WkD@yMPGN4E#poHyOVR z@jD;CY4~wSjmK{yevIP?{8YC?PNu0klLPAZCYxPH$485^TTRzU7PPn5Rp9A1IZw%r zQSf~Vs-Yw>##425fzu9srG24y+ucUqh-w#Uw9gn!yYv&6{4)HD)*p5KsqnSu-Y5*b z_=$xe519@^k(zQG{0DQ;@6JI_p!86B{*Z&dG>4v>a?p?F&~sM~`L-PN59H8OkVAfK z4*I+t^!swqOLEW`=b#Vfpg)(x|3`Aje<}z4OF8Jb<)FWigWjEkeoGGek8{xDIp}M1 z)VCprJm(D$e%a}15QgfXAId@hT@L-6b3FKECk`-AHWB#V9C{wgLEj1b7|c}L0#cct zcaDJ0xiCA0K^V(fR8J~O;H!dOWK5gqEO8%D>ff2A-@rWI7;6y|`#i(%Z)}aU`D5`w zH178s{*^UV{!lm?ZfuUl!_k_mWi64ma801TB`kSEa-hy1ZEN(0+cx`S;dn>8;csqh zjvJcZ(bn7$iMCpJprs`ev@n#g^3gzBXzl{T-+=OTG}0b!t8WR!=xrGZ?eV5)I1rM! 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SCI utilizes graph * python 2.7 **Python Libraries** -* [scikit-learn] >=0.19.0 +* [scikit-learn] >=0.19.0, <= 0.20 * [Numpy] >= 1.15 * [tqdm]>=4.24 +`Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4. Scikit-learn now requires Python 3.5 or newer.` + **C++ libraries** * [GSL] +### using Conda + +use conda-forge channel + +```sh +conda config --add channels conda-forge + +# +conda create -n sci_env python=2.7 + +# once created +conda activate sci_env + +# install own compilers +conda install compilers + +# save your env +mkdir -p envs +conda env export >envs/sci_env.yml + +``` + ## Installation ```sh -$ python setup.py +$ python setup.py install + +# clean +$ python setup.py clean + ``` ## Input format @@ -76,6 +104,9 @@ SCI output sub-compartments annotation into BED format with the following fields ## Test run + +`IS MISSING` + To preform test run for SCI please follow the following steps: 1. Go the Input_sample directory ```sh @@ -99,4 +130,4 @@ $ python sci.py -n test -f Input_sample/SCI_input.txt -r 100000 -g chromosome_si [scikit-learn]: http://scikit-learn.org/stable/ [Numpy]: http://www.numpy.org/ [tqdm]: https://pypi.org/project/tqdm/ -[GSL]: http://www.gnu.org/software/gsl/ \ No newline at end of file +[GSL]: http://www.gnu.org/software/gsl/ From 7ada871337e4bcf20cad98d02a4f6b563e94a08c Mon Sep 17 00:00:00 2001 From: Joseph Tran Date: Fri, 10 Apr 2020 23:28:42 +0200 Subject: [PATCH 5/6] forgot gsl install in conda env --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index d21db8a..0310fc8 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,9 @@ conda activate sci_env # install own compilers conda install compilers + +# install GSL +conda install gsl # save your env mkdir -p envs From 289393698033a9a67d0069d99d277e9e9c941292 Mon Sep 17 00:00:00 2001 From: Haitham Ashoor Date: Tue, 14 Apr 2020 11:17:16 -0400 Subject: [PATCH 6/6] Add dynamic path for library and include directory in the install script --- LINE/line | Bin 31784 -> 31784 bytes setup.py | 10 +++++++--- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/LINE/line b/LINE/line index 4aaeed8fcddcd714ad96db07c944fee962860781..d54e401b04eaff9863460787e445edc5ed901bdc 100755 GIT binary patch delta 186 zcmZ4SgK@1+VDUNz4E diff --git a/setup.py b/setup.py index f447169..432386c 100644 --- a/setup.py +++ b/setup.py @@ -7,12 +7,16 @@ VERSION = '0.1.0' -INCPATH="/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/sci_env/include" -LIBPATH="/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/sci_env/lib" + +CONDA_PATH = os.getenv("CONDA_PREFIX") +INCPATH = os.path.join(CONDA_PATH,"include") +LIBPATH=os.path.join(CONDA_PATH,"lib") + + LIBS="-lgsl -lgslcblas -lpthread -L{}".format(LIBPATH) def compile_line(): - compile_command = ("g++ -I{} LINE/line.cpp -o LINE/line {}".format(INCPATH, LIBS)) + compile_command = ("g++ LINE/line.cpp -I{} -o LINE/line {}".format(INCPATH,LIBS)) return_code = call(compile_command.split()) if return_code != 0: sys.exit(("LINE compilation has failed."